diff --git a/server/internal/daemon/execenv/reply_instructions.go b/server/internal/daemon/execenv/reply_instructions.go
index 58cdb3fb1a..9af2aca97f 100644
--- a/server/internal/daemon/execenv/reply_instructions.go
+++ b/server/internal/daemon/execenv/reply_instructions.go
@@ -199,3 +199,66 @@ func buildCommentReplyInstructionsSlim(provider, issueID, triggerCommentID strin
 		issueID, triggerCommentID,
 	)
 }
+
+// ThreadReplyTarget is one root-thread group a coalesced run must answer.
+// ThreadID labels the conversation (its root comment id); ParentID is the exact
+// `--parent` the agent must pass so its reply lands inside that thread.
+type ThreadReplyTarget struct {
+	ThreadID string
+	ParentID string
+}
+
+// BuildMultiThreadCommentReplyInstructions is the reply cookbook for a run whose
+// coalesced comments span MORE THAN ONE root thread (MUL-4348). It deliberately
+// overrides the general "post exactly one comment per run" guidance for this
+// specific run: three unrelated questions raised in three separate threads must
+// land as three in-thread answers, not one merged blob posted under a single
+// thread (or as a stray root comment).
+//
+// The grouping is computed server-side, so same-thread follow-ups never reach
+// here — they collapse to a single target upstream and take the ordinary
+// single-parent path. That is why the agent is told, unconditionally, to post
+// exactly one reply per listed thread and never more than one reply in the same
+// thread: the "multiple @mentions in one thread" case is already consolidated
+// before this instruction is emitted, so a per-thread fan-out cannot split it.
+//
+// Returns "" for fewer than two targets; callers keep the single-parent path.
+func BuildMultiThreadCommentReplyInstructions(issueID string, targets []ThreadReplyTarget) string {
+	if issueID == "" || len(targets) < 2 {
+		return ""
+	}
+
+	targetLines := ""
+	for _, tgt := range targets {
+		targetLines += fmt.Sprintf("- thread %s → reply with `--parent %s`\n", tgt.ThreadID, tgt.ParentID)
+	}
+
+	// File-hygiene guidance mirrors buildCommentReplyInstructionsSlim, but the
+	// agent must use a DISTINCT body file per thread so one reply's content can
+	// never leak into another's.
+	var cookbook string
+	if runtimeGOOS == "windows" {
+		cookbook = fmt.Sprintf(
+			"For EACH thread above, write that reply's body to its own UTF-8 file with your file-write tool, then post it with `--content-file` (do NOT use inline `--content` or a `--content-stdin` HEREDOC — see ## Comment Formatting above for why). Use one file per thread and remove each after posting:\n\n"+
+				"    multica issue comment add %s --parent <thread-parent-from-the-list-above> --content-file ./reply-1.md\n"+
+				"    Remove-Item ./reply-1.md\n\n",
+			issueID,
+		)
+	} else {
+		cookbook = fmt.Sprintf(
+			"For EACH thread above, write that reply's body to its own UTF-8 file with your file-write tool, then post it with `--content-file` (do NOT use inline `--content` or a `--content-stdin` HEREDOC — see ## Comment Formatting above for why). Use one file per thread and remove each after posting:\n\n"+
+				"    multica issue comment add %s --parent <thread-parent-from-the-list-above> --content-file ./reply-1.md\n"+
+				"    rm ./reply-1.md\n\n",
+			issueID,
+		)
+	}
+
+	return fmt.Sprintf(
+		"This run coalesced comments from %d DISTINCT threads. Post ONE reply per thread — %d replies in total — each threaded under its own conversation. This OVERRIDES the general \"post exactly one comment per run\" guidance: for THIS run multiple replies are required and correct. Do NOT merge separate threads into a single comment, and do NOT post more than one reply in the same thread.\n\n"+
+			"Reply targets (use the exact `--parent` for each — do NOT reuse `--parent` values from previous turns in this session):\n"+
+			"%s\n"+
+			"%s"+
+			"Do NOT write literal `\\n` escapes to simulate line breaks; each file preserves real newlines.\n",
+		len(targets), len(targets), targetLines, cookbook,
+	)
+}
diff --git a/server/internal/daemon/prompt.go b/server/internal/daemon/prompt.go
index c683702d64..930e589998 100644
--- a/server/internal/daemon/prompt.go
+++ b/server/internal/daemon/prompt.go
@@ -220,10 +220,76 @@ func buildCommentPrompt(task Task, provider string) string {
 	} else {
 		fmt.Fprintf(&b, "Read the discussion: `multica issue comment list %s --recent 10 --output json` (resolved threads come back folded — `--full` to expand).\n\n", task.IssueID)
 	}
-	b.WriteString(execenv.BuildCommentReplyInstructions(provider, task.IssueID, task.TriggerCommentID))
+	// Reply routing. When this run coalesced comments spanning MORE THAN ONE
+	// root thread, answer each thread in its own thread instead of dumping one
+	// merged comment (MUL-4348). Same-thread follow-ups collapse to a single
+	// group upstream, so they keep the ordinary single-parent path below and can
+	// never be split into duplicate replies.
+	if targets := commentReplyThreads(task); len(targets) >= 2 {
+		b.WriteString(execenv.BuildMultiThreadCommentReplyInstructions(task.IssueID, targets))
+	} else {
+		b.WriteString(execenv.BuildCommentReplyInstructions(provider, task.IssueID, task.TriggerCommentID))
+	}
 	return b.String()
 }
 
+// commentReplyThreads groups this run's trigger + coalesced comments by their
+// root thread, in first-seen order (coalesced comments oldest-first, the newest
+// trigger last). A run that coalesced several @mentions from the SAME thread
+// yields a single group, so same-thread follow-ups get exactly one consolidated
+// reply and can never be split into duplicates; comments from different root
+// threads yield one group each so the agent replies inside each thread instead
+// of merging them into one blob (MUL-4348).
+//
+// The trigger's own thread replies under the trigger comment itself, matching
+// the long-standing single-thread behaviour (--parent = trigger comment id);
+// every other thread replies under its root comment id. Returns nil when there
+// is no trigger or only a single distinct thread — the caller then keeps the
+// existing single-parent reply path unchanged.
+func commentReplyThreads(task Task) []execenv.ThreadReplyTarget {
+	if task.TriggerCommentID == "" {
+		return nil
+	}
+	// A comment with no explicit thread id is a root comment: it is its own
+	// thread, so fall back to the comment id itself as the thread key.
+	threadKey := func(threadID, commentID string) string {
+		if threadID != "" {
+			return threadID
+		}
+		return commentID
+	}
+
+	order := make([]string, 0, len(task.CoalescedComments)+1)
+	parentByThread := make(map[string]string, len(task.CoalescedComments)+1)
+	note := func(threadID, parentID string) {
+		if _, ok := parentByThread[threadID]; !ok {
+			order = append(order, threadID)
+		}
+		parentByThread[threadID] = parentID
+	}
+
+	// Coalesced (older) comments first: each replies under its own thread root.
+	for _, cc := range task.CoalescedComments {
+		tid := threadKey(cc.ThreadID, cc.ID)
+		if _, ok := parentByThread[tid]; ok {
+			continue // thread already represented; keep its first parent
+		}
+		note(tid, tid)
+	}
+	// The newest trigger last: its thread replies under the trigger comment,
+	// overriding any coalesced comment that shared the trigger's thread.
+	note(threadKey(task.TriggerThreadID, task.TriggerCommentID), task.TriggerCommentID)
+
+	if len(order) <= 1 {
+		return nil
+	}
+	targets := make([]execenv.ThreadReplyTarget, 0, len(order))
+	for _, tid := range order {
+		targets = append(targets, execenv.ThreadReplyTarget{ThreadID: tid, ParentID: parentByThread[tid]})
+	}
+	return targets
+}
+
 // buildChatPrompt constructs a prompt for interactive chat tasks.
 func buildChatPrompt(task Task) string {
 	// Proactive self-introduction: the agent was just created and is opening the
diff --git a/server/internal/daemon/prompt_test.go b/server/internal/daemon/prompt_test.go
index 9b60ede261..9ed01d7f7f 100644
--- a/server/internal/daemon/prompt_test.go
+++ b/server/internal/daemon/prompt_test.go
@@ -676,3 +676,147 @@ func TestBuildCommentPromptCoalescedIDsOnlyFallback(t *testing.T) {
 		}
 	}
 }
+
+// TestCommentReplyThreadsGrouping pins the server-side grouping that drives
+// per-thread reply routing (MUL-4348). The invariants:
+//   - three distinct root threads → three targets, each replying to its own
+//     thread (the trigger's thread replies under the trigger comment itself).
+//   - multiple coalesced follow-ups in the SAME thread → a single group, so the
+//     caller keeps the single-parent path and the reply is never duplicated.
+//   - no coalesced comments (ordinary single comment) → nil.
+func TestCommentReplyThreadsGrouping(t *testing.T) {
+	t.Run("three distinct root threads fan out", func(t *testing.T) {
+		task := Task{
+			TriggerCommentID: "c3",
+			TriggerThreadID:  "c3", // a root comment is its own thread
+			CoalescedComments: []CoalescedCommentData{
+				{ID: "c1", ThreadID: "c1", Content: "背一首宋词"},
+				{ID: "c2", ThreadID: "c2", Content: "毛泽东诗词背一首"},
+			},
+		}
+		targets := commentReplyThreads(task)
+		if len(targets) != 3 {
+			t.Fatalf("want 3 targets, got %d: %+v", len(targets), targets)
+		}
+		wantParent := map[string]string{"c1": "c1", "c2": "c2", "c3": "c3"}
+		for _, tgt := range targets {
+			if wantParent[tgt.ThreadID] != tgt.ParentID {
+				t.Errorf("thread %s: parent = %s, want %s", tgt.ThreadID, tgt.ParentID, wantParent[tgt.ThreadID])
+			}
+		}
+	})
+
+	t.Run("same-thread follow-ups consolidate to a single group", func(t *testing.T) {
+		task := Task{
+			TriggerCommentID: "c3",
+			TriggerThreadID:  "thread-A",
+			CoalescedComments: []CoalescedCommentData{
+				{ID: "c1", ThreadID: "thread-A", Content: "追问 1"},
+				{ID: "c2", ThreadID: "thread-A", Content: "追问 2"},
+			},
+		}
+		if targets := commentReplyThreads(task); targets != nil {
+			t.Fatalf("same-thread follow-ups must not fan out; got %d targets: %+v", len(targets), targets)
+		}
+	})
+
+	t.Run("mixed: trigger thread plus one other thread", func(t *testing.T) {
+		task := Task{
+			TriggerCommentID: "c3",
+			TriggerThreadID:  "thread-A",
+			CoalescedComments: []CoalescedCommentData{
+				{ID: "c1", ThreadID: "thread-A", Content: "same-thread follow-up"},
+				{ID: "c2", ThreadID: "thread-B", Content: "other thread"},
+			},
+		}
+		targets := commentReplyThreads(task)
+		if len(targets) != 2 {
+			t.Fatalf("want 2 targets (thread-A, thread-B), got %d: %+v", len(targets), targets)
+		}
+		got := map[string]string{}
+		for _, tgt := range targets {
+			got[tgt.ThreadID] = tgt.ParentID
+		}
+		// The trigger's own thread replies under the trigger comment, not its root.
+		if got["thread-A"] != "c3" {
+			t.Errorf("trigger thread parent = %q, want c3 (the trigger comment)", got["thread-A"])
+		}
+		if got["thread-B"] != "thread-B" {
+			t.Errorf("other thread parent = %q, want its root thread-B", got["thread-B"])
+		}
+	})
+
+	t.Run("no coalesced comments → nil", func(t *testing.T) {
+		task := Task{TriggerCommentID: "c1", TriggerThreadID: "thread-A"}
+		if targets := commentReplyThreads(task); targets != nil {
+			t.Fatalf("ordinary single-comment run must not fan out; got %+v", targets)
+		}
+	})
+}
+
+// TestBuildCommentPromptCrossThreadFansOutReplies is the end-to-end prompt
+// assertion for the screenshot scenario: three separate root comments coalesced
+// into one run must produce a per-thread reply plan (one reply per thread),
+// explicitly overriding the "one comment per run" rule, instead of the single
+// --parent cookbook.
+func TestBuildCommentPromptCrossThreadFansOutReplies(t *testing.T) {
+	task := Task{
+		IssueID:               "issue-xthread-2",
+		TriggerCommentID:      "c3",
+		TriggerThreadID:       "c3",
+		TriggerCommentContent: "莎士比亚名言来一句",
+		TriggerAuthorType:     "member",
+		CoalescedCommentIDs:   []string{"c1", "c2"},
+		CoalescedComments: []CoalescedCommentData{
+			{ID: "c1", ThreadID: "c1", AuthorType: "member", AuthorName: "Yushen", Content: "背一首宋词", CreatedAt: "2026-07-10T01:00:00Z"},
+			{ID: "c2", ThreadID: "c2", AuthorType: "member", AuthorName: "Yushen", Content: "毛泽东诗词背一首", CreatedAt: "2026-07-10T02:00:00Z"},
+		},
+	}
+	out := BuildPrompt(task, "claude")
+
+	for _, want := range []string{
+		"3 DISTINCT threads",
+		"Post ONE reply per thread",
+		"OVERRIDES",
+		"--parent c1",
+		"--parent c2",
+		"--parent c3",
+	} {
+		if !strings.Contains(out, want) {
+			t.Errorf("cross-thread prompt must contain %q, got:\n%s", want, out)
+		}
+	}
+	// The single-parent cookbook must NOT be used when fanning out.
+	if strings.Contains(out, "always use the trigger comment ID below") {
+		t.Errorf("cross-thread prompt must not emit the single-parent reply cookbook, got:\n%s", out)
+	}
+}
+
+// TestBuildCommentPromptSameThreadKeepsSingleReply pins the hard requirement:
+// multiple @mentions coalesced from the SAME thread must keep the ordinary
+// single-parent reply path (one reply, under the trigger comment) and must NOT
+// trigger the multi-thread fan-out.
+func TestBuildCommentPromptSameThreadKeepsSingleReply(t *testing.T) {
+	task := Task{
+		IssueID:               "issue-samethread-1",
+		TriggerCommentID:      "c3",
+		TriggerThreadID:       "thread-A",
+		TriggerCommentContent: "追问 3",
+		TriggerAuthorType:     "member",
+		CoalescedCommentIDs:   []string{"c1", "c2"},
+		CoalescedComments: []CoalescedCommentData{
+			{ID: "c1", ThreadID: "thread-A", AuthorType: "member", AuthorName: "Yushen", Content: "追问 1", CreatedAt: "2026-07-10T01:00:00Z"},
+			{ID: "c2", ThreadID: "thread-A", AuthorType: "member", AuthorName: "Yushen", Content: "追问 2", CreatedAt: "2026-07-10T02:00:00Z"},
+		},
+	}
+	out := BuildPrompt(task, "claude")
+
+	if strings.Contains(out, "DISTINCT threads") {
+		t.Errorf("same-thread coalescing must not emit the multi-thread fan-out block, got:\n%s", out)
+	}
+	// The single-parent cookbook is used, threading the one reply under the
+	// trigger comment.
+	if !strings.Contains(out, "--parent c3 --content-file ./reply.md") {
+		t.Errorf("same-thread run must keep the single --parent=trigger reply cookbook, got:\n%s", out)
+	}
+}