diff --git a/pkg/memory/jsonl.go b/pkg/memory/jsonl.go
index 072795bc9..492205114 100644
--- a/pkg/memory/jsonl.go
+++ b/pkg/memory/jsonl.go
@@ -10,6 +10,7 @@ import (
 	"log"
 	"os"
 	"path/filepath"
+	"sort"
 	"strings"
 	"sync"
 	"time"
@@ -406,12 +407,9 @@ func (s *JSONLStore) promoteAliasHistoryLocked(
 }
 
 func (s *JSONLStore) sessionHasVisibleContentLocked(sessionKey string, meta SessionMeta) (bool, error) {
-	if meta.Count-meta.Skip > 0 || strings.TrimSpace(meta.Summary) != "" {
+	if strings.TrimSpace(meta.Summary) != "" {
 		return true, nil
 	}
-	if meta.Count != 0 || meta.Skip != 0 {
-		return false, nil
-	}
 	history, err := readMessages(s.jsonlPath(sessionKey), meta.Skip)
 	if err != nil {
 		return false, err
@@ -498,28 +496,44 @@ func readMessages(path string, skip int) ([]providers.Message, error) {
 	return msgs, nil
 }
 
-// countLines counts the total number of non-empty lines in a .jsonl file.
-// Used by TruncateHistory to reconcile a stale meta.Count without
-// the overhead of unmarshaling every message.
-func countLines(path string) (int, error) {
+// scanRetainedMessageLines returns the total number of non-empty raw JSONL
+// lines plus the raw line numbers that survive readMessages filtering.
+// TruncateHistory uses this to compute keepLast against retained messages
+// while preserving the raw-line skip offset stored in metadata.
+func scanRetainedMessageLines(path string) (int, []int, error) {
 	f, err := os.Open(path)
 	if os.IsNotExist(err) {
-		return 0, nil
+		return 0, []int{}, nil
 	}
 	if err != nil {
-		return 0, fmt.Errorf("memory: open jsonl: %w", err)
+		return 0, nil, fmt.Errorf("memory: open jsonl: %w", err)
 	}
 	defer f.Close()
 
-	n := 0
+	rawCount := 0
+	retained := make([]int, 0)
 	scanner := bufio.NewScanner(f)
 	scanner.Buffer(make([]byte, 0, 64*1024), maxLineSize)
 	for scanner.Scan() {
-		if len(scanner.Bytes()) > 0 {
-			n++
+		line := scanner.Bytes()
+		if len(line) == 0 {
+			continue
 		}
+		rawCount++
+
+		var msg providers.Message
+		if err := json.Unmarshal(line, &msg); err != nil {
+			continue
+		}
+		if messageutil.IsTransientAssistantThoughtMessage(msg) {
+			continue
+		}
+		retained = append(retained, rawCount)
 	}
-	return n, scanner.Err()
+	if err := scanner.Err(); err != nil {
+		return 0, nil, err
+	}
+	return rawCount, retained, nil
 }
 
 func (s *JSONLStore) AddMessage(
@@ -663,24 +677,26 @@ func (s *JSONLStore) TruncateHistory(
 		return err
 	}
 
-	// Always reconcile meta.Count with the actual line count on disk.
-	// A crash between the JSONL append and the meta update in addMsg
-	// leaves meta.Count stale (e.g. file has 101 lines but meta says
-	// 100). Counting lines is cheap — no unmarshal, just a scan — and
-	// TruncateHistory is not a hot path, so always re-count.
-	n, countErr := countLines(s.jsonlPath(sessionKey))
-	if countErr != nil {
-		return countErr
+	rawCount, retainedRawLines, scanErr := scanRetainedMessageLines(s.jsonlPath(sessionKey))
+	if scanErr != nil {
+		return scanErr
 	}
-	meta.Count = n
-
-	if keepLast <= 0 {
+	meta.Count = rawCount
+	if meta.Skip > meta.Count {
 		meta.Skip = meta.Count
-	} else {
-		effective := meta.Count - meta.Skip
-		if keepLast < effective {
-			meta.Skip = meta.Count - keepLast
-		}
+	}
+
+	activeStart := sort.Search(len(retainedRawLines), func(i int) bool {
+		return retainedRawLines[i] > meta.Skip
+	})
+	activeRetainedCount := len(retainedRawLines) - activeStart
+
+	switch {
+	case keepLast <= 0 || activeRetainedCount == 0:
+		meta.Skip = meta.Count
+	case keepLast < activeRetainedCount:
+		activeRawLines := retainedRawLines[activeStart:]
+		meta.Skip = activeRawLines[activeRetainedCount-keepLast-1]
 	}
 	meta.UpdatedAt = time.Now()
 
diff --git a/pkg/memory/jsonl_test.go b/pkg/memory/jsonl_test.go
index f72b84804..3a7b98130 100644
--- a/pkg/memory/jsonl_test.go
+++ b/pkg/memory/jsonl_test.go
@@ -9,6 +9,7 @@ import (
 	"strings"
 	"sync"
 	"testing"
+	"time"
 
 	"github.com/sipeed/picoclaw/pkg/providers"
 )
@@ -795,6 +796,56 @@ func TestTruncateHistory_StaleMetaCount(t *testing.T) {
 	}
 }
 
+func TestTruncateHistory_IgnoresTransientThoughtForKeepLast(t *testing.T) {
+	store := newTestStore(t)
+	ctx := context.Background()
+	sessionKey := "transient-keep-last"
+	now := time.Now()
+
+	rawJSONL := strings.Join([]string{
+		`{"role":"user","content":"a"}`,
+		`{"role":"assistant","content":"b"}`,
+		`{"role":"assistant","content":"","reasoning_content":"dangling thought"}`,
+		`{"role":"user","content":"c"}`,
+		`{"role":"assistant","content":"d"}`,
+	}, "\n") + "\n"
+	if err := os.WriteFile(store.jsonlPath(sessionKey), []byte(rawJSONL), 0o644); err != nil {
+		t.Fatalf("WriteFile(jsonl): %v", err)
+	}
+	if err := store.writeMeta(sessionKey, SessionMeta{
+		Key:       sessionKey,
+		Count:     5,
+		Skip:      0,
+		CreatedAt: now,
+		UpdatedAt: now,
+	}); err != nil {
+		t.Fatalf("writeMeta: %v", err)
+	}
+
+	if err := store.TruncateHistory(ctx, sessionKey, 2); err != nil {
+		t.Fatalf("TruncateHistory: %v", err)
+	}
+
+	history, err := store.GetHistory(ctx, sessionKey)
+	if err != nil {
+		t.Fatalf("GetHistory: %v", err)
+	}
+	if len(history) != 2 {
+		t.Fatalf("expected 2 retained messages, got %d", len(history))
+	}
+	if history[0].Content != "c" || history[1].Content != "d" {
+		t.Fatalf("kept history = %+v, want c,d", history)
+	}
+
+	meta, err := store.readMeta(sessionKey)
+	if err != nil {
+		t.Fatalf("readMeta: %v", err)
+	}
+	if meta.Skip != 2 {
+		t.Fatalf("meta.Skip = %d, want 2 raw lines skipped", meta.Skip)
+	}
+}
+
 func TestCrashRecovery_PartialLine(t *testing.T) {
 	store := newTestStore(t)
 	ctx := context.Background()
diff --git a/web/backend/api/session.go b/web/backend/api/session.go
index 7bfe43026..287892cd2 100644
--- a/web/backend/api/session.go
+++ b/web/backend/api/session.go
@@ -155,6 +155,9 @@ func (h *Handler) readSessionMessages(path string, skip int) ([]providers.Messag
 		if err := json.Unmarshal(line, &msg); err != nil {
 			continue
 		}
+		if messageutil.IsTransientAssistantThoughtMessage(msg) {
+			continue
+		}
 		msgs = append(msgs, msg)
 	}
 	if err := scanner.Err(); err != nil {
diff --git a/web/backend/api/session_test.go b/web/backend/api/session_test.go
index f8fb2483a..8d92760d2 100644
--- a/web/backend/api/session_test.go
+++ b/web/backend/api/session_test.go
@@ -8,6 +8,7 @@ import (
 	"path/filepath"
 	"strings"
 	"testing"
+	"time"
 
 	"github.com/sipeed/picoclaw/pkg/config"
 	"github.com/sipeed/picoclaw/pkg/memory"
@@ -101,6 +102,64 @@ func TestHandleListSessions_JSONLStorage(t *testing.T) {
 	}
 }
 
+func TestHandleListSessions_TransientThoughtDoesNotInflateMessageCount(t *testing.T) {
+	configPath, cleanup := setupOAuthTestEnv(t)
+	defer cleanup()
+
+	dir := sessionsTestDir(t, configPath)
+	sessionKey := legacyPicoSessionPrefix + "history-jsonl-transient"
+	base := filepath.Join(dir, sanitizeSessionKey(sessionKey))
+	now := time.Now().UTC()
+
+	rawJSONL := strings.Join([]string{
+		`{"role":"user","content":"keep me"}`,
+		`{"role":"assistant","content":"","reasoning_content":"dangling thought"}`,
+		`{"role":"assistant","content":"and me"}`,
+	}, "\n") + "\n"
+	if err := os.WriteFile(base+".jsonl", []byte(rawJSONL), 0o644); err != nil {
+		t.Fatalf("WriteFile(jsonl) error = %v", err)
+	}
+	metaData, err := json.Marshal(memory.SessionMeta{
+		Key:       sessionKey,
+		Count:     3,
+		Skip:      0,
+		CreatedAt: now,
+		UpdatedAt: now,
+	})
+	if err != nil {
+		t.Fatalf("Marshal(meta) error = %v", err)
+	}
+	if err := os.WriteFile(base+".meta.json", metaData, 0o644); err != nil {
+		t.Fatalf("WriteFile(meta) error = %v", err)
+	}
+
+	h := NewHandler(configPath)
+	mux := http.NewServeMux()
+	h.RegisterRoutes(mux)
+
+	rec := httptest.NewRecorder()
+	req := httptest.NewRequest(http.MethodGet, "/api/sessions", nil)
+	mux.ServeHTTP(rec, req)
+
+	if rec.Code != http.StatusOK {
+		t.Fatalf("status = %d, want %d, body=%s", rec.Code, http.StatusOK, rec.Body.String())
+	}
+
+	var items []sessionListItem
+	if err := json.Unmarshal(rec.Body.Bytes(), &items); err != nil {
+		t.Fatalf("Unmarshal() error = %v", err)
+	}
+	if len(items) != 1 {
+		t.Fatalf("len(items) = %d, want 1", len(items))
+	}
+	if items[0].ID != "history-jsonl-transient" {
+		t.Fatalf("items[0].ID = %q, want %q", items[0].ID, "history-jsonl-transient")
+	}
+	if items[0].MessageCount != 2 {
+		t.Fatalf("items[0].MessageCount = %d, want 2 after dropping transient thought", items[0].MessageCount)
+	}
+}
+
 func TestHandleListSessions_TitleUsesFirstUserMessage(t *testing.T) {
 	configPath, cleanup := setupOAuthTestEnv(t)
 	defer cleanup()