diff --git a/internal/writer/footer.go b/internal/writer/footer.go
index f0565a8..c8a5ab1 100644
--- a/internal/writer/footer.go
+++ b/internal/writer/footer.go
@@ -68,3 +68,23 @@ func whatIsBlock(opts FooterOptions) string {
 func HasMarker(content []byte) bool {
 	return strings.Contains(string(content), MarkerStart)
 }
+
+// stripGeneratedMarker 把首个 `<!-- Generated by stdagent ... -->` 注释整体替换为稳定占位符
+//
+// 用于 writer.Apply 内容等价性比较：marker 含 version + timestamp，每次 sync 都会变，
+// 不归一化会导致即使源文档未变也整文件重写，污染 git diff。
+//
+// 仅替换首个 MarkerStart 注释；MarkerEnd 不带变量值无需处理。
+func stripGeneratedMarker(content []byte) []byte {
+	s := string(content)
+	start := strings.Index(s, MarkerStart)
+	if start < 0 {
+		return content
+	}
+	rel := strings.Index(s[start:], "-->")
+	if rel < 0 {
+		return content
+	}
+	end := start + rel + len("-->")
+	return []byte(s[:start] + "<!-- stdagent-marker -->" + s[end:])
+}
diff --git a/internal/writer/writer.go b/internal/writer/writer.go
index 6d6939e..ebcfdcb 100644
--- a/internal/writer/writer.go
+++ b/internal/writer/writer.go
@@ -38,6 +38,14 @@ func (w *Writer) Apply(plan *Plan) (written, skipped int, err error) {
 			skipped++
 			continue
 		}
+		// marker 含每次 sync 不同的 timestamp（footer.HeaderComment 注入 GeneratedAt），
+		// 归一化 marker 后再比一次：源文档未变则不重写，避免污染 git diff / mtime。
+		if len(exist) > 0 && bytes.Equal(stripGeneratedMarker(exist), stripGeneratedMarker(op.Content)) {
+			op.Skip = true
+			op.Reason = "unchanged"
+			skipped++
+			continue
+		}
 		if w.DryRun {
 			continue
 		}
diff --git a/internal/writer/writer_test.go b/internal/writer/writer_test.go
index 1573d61..54cccad 100644
--- a/internal/writer/writer_test.go
+++ b/internal/writer/writer_test.go
@@ -246,6 +246,73 @@ func TestApplyMixedWrittenAndSkipped(t *testing.T) {
 	}
 }
 
+func TestApplySkipsWhenOnlyMarkerTimestampDiffers(t *testing.T) {
+	tmp := t.TempDir()
+	w := NewWriter(tmp, false)
+
+	oldHeader := "<!-- Generated by stdagent v0.1.0 at 2026-01-01T00:00:00Z. Source: .stdai/standards/rules/style.md. Run `stdagent sync` to regenerate. Do not edit by hand. -->\n"
+	newHeader := "<!-- Generated by stdagent v0.1.0 at 2026-05-10T08:32:11Z. Source: .stdai/standards/rules/style.md. Run `stdagent sync` to regenerate. Do not edit by hand. -->\n"
+	body := "# Style\n\nbody content\n<!-- /Generated by stdagent -->\n"
+	mustWrite(t, filepath.Join(tmp, "out.md"), oldHeader+body)
+
+	statBefore, _ := os.Stat(filepath.Join(tmp, "out.md"))
+
+	plan := &Plan{
+		Files: []FileOp{
+			{Path: "out.md", Content: []byte(newHeader + body), Marker: true},
+		},
+	}
+	written, skipped, err := w.Apply(plan)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if written != 0 || skipped != 1 {
+		t.Errorf("written=%d skipped=%d, want 0/1", written, skipped)
+	}
+	if !plan.Files[0].Skip || plan.Files[0].Reason != "unchanged" {
+		t.Errorf("op = %+v", plan.Files[0])
+	}
+	statAfter, _ := os.Stat(filepath.Join(tmp, "out.md"))
+	if !statBefore.ModTime().Equal(statAfter.ModTime()) {
+		t.Errorf("mtime should not change: before=%v after=%v", statBefore.ModTime(), statAfter.ModTime())
+	}
+	got, _ := os.ReadFile(filepath.Join(tmp, "out.md"))
+	if string(got) != oldHeader+body {
+		t.Errorf("file content should be untouched, got %q", got)
+	}
+}
+
+func TestApplyWritesWhenBodyChangesEvenIfMarkerSame(t *testing.T) {
+	tmp := t.TempDir()
+	w := NewWriter(tmp, false)
+	header := "<!-- Generated by stdagent v0.1.0 at 2026-01-01T00:00:00Z. Source: .stdai/standards/rules/style.md. Run `stdagent sync` to regenerate. Do not edit by hand. -->\n"
+	mustWrite(t, filepath.Join(tmp, "out.md"), header+"# Old\n")
+
+	plan := &Plan{
+		Files: []FileOp{
+			{Path: "out.md", Content: []byte(header + "# New\n"), Marker: true},
+		},
+	}
+	written, skipped, _ := w.Apply(plan)
+	if written != 1 || skipped != 0 {
+		t.Errorf("written=%d skipped=%d, want 1/0", written, skipped)
+	}
+}
+
+func TestStripGeneratedMarker(t *testing.T) {
+	src := []byte("<!-- Generated by stdagent v0.1.0 at 2026-05-10T08:32:11Z. Source: x. -->\nbody\n")
+	got := stripGeneratedMarker(src)
+	want := "<!-- stdagent-marker -->\nbody\n"
+	if string(got) != want {
+		t.Errorf("stripGeneratedMarker = %q, want %q", got, want)
+	}
+
+	plain := []byte("# no marker here\nbody\n")
+	if string(stripGeneratedMarker(plain)) != string(plain) {
+		t.Error("content without marker should be returned as-is")
+	}
+}
+
 func TestApplySkipPreSet(t *testing.T) {
 	tmp := t.TempDir()
 	w := NewWriter(tmp, false)