diff --git a/br/pkg/lightning/restore/checksum.go b/br/pkg/lightning/restore/checksum.go
index 5b7a5b1501af4..e9519b65170cf 100644
--- a/br/pkg/lightning/restore/checksum.go
+++ b/br/pkg/lightning/restore/checksum.go
@@ -279,12 +279,8 @@ func newTiKVChecksumManager(client kv.Client, pdClient pd.Client, distSQLScanCon
 	}
 }
 
-func (e *tikvChecksumManager) checksumDB(ctx context.Context, tableInfo *checkpoints.TidbTableInfo) (*RemoteChecksum, error) {
-	physicalTS, logicalTS, err := e.manager.pdClient.GetTS(ctx)
-	if err != nil {
-		return nil, errors.Annotate(err, "fetch tso from pd failed")
-	}
-	executor, err := checksum.NewExecutorBuilder(tableInfo.Core, oracle.ComposeTS(physicalTS, logicalTS)).
+func (e *tikvChecksumManager) checksumDB(ctx context.Context, tableInfo *checkpoints.TidbTableInfo, ts uint64) (*RemoteChecksum, error) {
+	executor, err := checksum.NewExecutorBuilder(tableInfo.Core, ts).
 		SetConcurrency(e.distSQLScanConcurrency).
 		Build()
 	if err != nil {
@@ -327,12 +323,16 @@ func (e *tikvChecksumManager) checksumDB(ctx context.Context, tableInfo *checkpo
 
 func (e *tikvChecksumManager) Checksum(ctx context.Context, tableInfo *checkpoints.TidbTableInfo) (*RemoteChecksum, error) {
 	tbl := common.UniqueTable(tableInfo.DB, tableInfo.Name)
-	err := e.manager.addOneJob(ctx, tbl, oracle.ComposeTS(time.Now().Unix()*1000, 0))
+	physicalTS, logicalTS, err := e.manager.pdClient.GetTS(ctx)
 	if err != nil {
+		return nil, errors.Annotate(err, "fetch tso from pd failed")
+	}
+	ts := oracle.ComposeTS(physicalTS, logicalTS)
+	if err := e.manager.addOneJob(ctx, tbl, ts); err != nil {
 		return nil, errors.Trace(err)
 	}
 
-	return e.checksumDB(ctx, tableInfo)
+	return e.checksumDB(ctx, tableInfo, ts)
 }
 
 type tableChecksumTS struct {
diff --git a/br/pkg/lightning/restore/checksum_test.go b/br/pkg/lightning/restore/checksum_test.go
index 6a9f334b31f9a..b0addcd04f15d 100644
--- a/br/pkg/lightning/restore/checksum_test.go
+++ b/br/pkg/lightning/restore/checksum_test.go
@@ -25,6 +25,7 @@ import (
 	"github.com/pingcap/tipb/go-tipb"
 	"github.com/tikv/client-go/v2/oracle"
 	pd "github.com/tikv/pd/client"
+	uatomic "go.uber.org/atomic"
 )
 
 var _ = Suite(&checksumSuite{})
@@ -169,10 +170,16 @@ func (s *checksumSuite) TestDoChecksumWithTikv(c *C) {
 	for i := 0; i <= maxErrorRetryCount; i++ {
 		kvClient.maxErrCount = i
 		kvClient.curErrCount = 0
+		var checksumTS uint64
+		kvClient.onSendReq = func(req *kv.Request) {
+			checksumTS = req.StartTs
+		}
 		checksumExec := &tikvChecksumManager{manager: newGCTTLManager(pdClient), client: kvClient}
-		startTS := oracle.ComposeTS(time.Now().Unix()*1000, 0)
-		ctx := context.WithValue(context.Background(), &checksumManagerKey, checksumExec)
-		_, err = DoChecksum(ctx, &TidbTableInfo{DB: "test", Name: "t", Core: tableInfo})
+		ctx := context.Background()
+		physicalTS, logicalTS, err := pdClient.GetTS(ctx)
+		c.Assert(err, IsNil)
+		subCtx := context.WithValue(ctx, &checksumManagerKey, checksumExec)
+		_, err = DoChecksum(subCtx, &TidbTableInfo{DB: "test", Name: "t", Core: tableInfo})
 		// with max error retry < maxErrorRetryCount, the checksum can success
 		if i >= maxErrorRetryCount {
 			c.Assert(err, ErrorMatches, "tikv timeout")
@@ -184,7 +191,9 @@ func (s *checksumSuite) TestDoChecksumWithTikv(c *C) {
 		// after checksum, safepint should be small than start ts
 		ts := pdClient.currentSafePoint()
 		// 1ms for the schedule deviation
+		startTS := oracle.ComposeTS(physicalTS+1, logicalTS)
 		c.Assert(ts <= startTS+1, IsTrue)
+		c.Assert(checksumTS >= ts, IsTrue)
 		c.Assert(atomic.LoadUint32(&checksumExec.manager.started) > 0, IsTrue)
 	}
 }
@@ -215,15 +224,15 @@ func (s *checksumSuite) TestDoChecksumWithErrorAndLongOriginalLifetime(c *C) {
 
 type safePointTTL struct {
 	safePoint uint64
-	// ttl is the last timestamp this safe point is valid
-	ttl int64
+	expiredAt int64
 }
 
 type testPDClient struct {
 	sync.Mutex
 	pd.Client
-	count       int32
-	gcSafePoint []safePointTTL
+	count            int32
+	gcSafePoint      []safePointTTL
+	logicalTSCounter uatomic.Uint64
 }
 
 func (c *testPDClient) currentSafePoint() uint64 {
@@ -231,7 +240,7 @@ func (c *testPDClient) currentSafePoint() uint64 {
 	c.Lock()
 	defer c.Unlock()
 	for _, s := range c.gcSafePoint {
-		if s.ttl > ts {
+		if s.expiredAt > ts {
 			return s.safePoint
 		}
 	}
@@ -239,7 +248,9 @@ func (c *testPDClient) currentSafePoint() uint64 {
 }
 
 func (c *testPDClient) GetTS(ctx context.Context) (int64, int64, error) {
-	return time.Now().Unix(), 0, nil
+	physicalTS := time.Now().UnixNano() / 1e6
+	logicalTS := oracle.ExtractLogical(c.logicalTSCounter.Inc())
+	return physicalTS, logicalTS, nil
 }
 
 func (c *testPDClient) UpdateServiceGCSafePoint(ctx context.Context, serviceID string, ttl int64, safePoint uint64) (uint64, error) {
@@ -253,13 +264,13 @@ func (c *testPDClient) UpdateServiceGCSafePoint(ctx context.Context, serviceID s
 	})
 	sp := c.gcSafePoint
 	ttlEnd := time.Now().Unix() + ttl
-	spTTL := safePointTTL{safePoint: safePoint, ttl: ttlEnd}
+	spTTL := safePointTTL{safePoint: safePoint, expiredAt: ttlEnd}
 	switch {
 	case idx >= len(sp):
 		c.gcSafePoint = append(c.gcSafePoint, spTTL)
 	case sp[idx].safePoint == safePoint:
-		if ttlEnd > sp[idx].ttl {
-			sp[idx].ttl = ttlEnd
+		if ttlEnd > sp[idx].expiredAt {
+			sp[idx].expiredAt = ttlEnd
 		}
 	default:
 		c.gcSafePoint = append(append(sp[:idx], spTTL), sp[idx:]...)
@@ -385,8 +396,9 @@ func (r *mockResultSubset) RespTime() time.Duration {
 
 type mockChecksumKVClient struct {
 	kv.Client
-	checksum tipb.ChecksumResponse
-	respDur  time.Duration
+	checksum  tipb.ChecksumResponse
+	respDur   time.Duration
+	onSendReq func(req *kv.Request)
 	// return error count before return success
 	maxErrCount int
 	curErrCount int
@@ -394,6 +406,9 @@ type mockChecksumKVClient struct {
 
 // a mock client for checksum request
 func (c *mockChecksumKVClient) Send(ctx context.Context, req *kv.Request, vars interface{}, sessionMemTracker *memory.Tracker, enabledRateLimitAction bool, eventCb trxevents.EventCallback) kv.Response {
+	if c.onSendReq != nil {
+		c.onSendReq(req)
+	}
 	if c.curErrCount < c.maxErrCount {
 		c.curErrCount++
 		return &mockErrorResponse{err: "tikv timeout"}