diff --git a/server/grpc_service.go b/server/grpc_service.go
index ac8b85ac99c..3d1d4b727c4 100644
--- a/server/grpc_service.go
+++ b/server/grpc_service.go
@@ -564,7 +564,7 @@ func (s *Server) UpdateGCSafePoint(ctx context.Context, request *pdpb.UpdateGCSa
 		}
 		log.Infof("updated gc safe point to %d", newSafePoint)
 	} else if newSafePoint < oldSafePoint {
-		log.Warn("trying to update gc safe point from %d to %d", oldSafePoint, newSafePoint)
+		log.Warnf("trying to update gc safe point from %d to %d", oldSafePoint, newSafePoint)
 		newSafePoint = oldSafePoint
 	}
 
diff --git a/server/tso.go b/server/tso.go
index fe978b858cd..872d9315691 100644
--- a/server/tso.go
+++ b/server/tso.go
@@ -57,8 +57,8 @@ func (s *Server) loadTimestamp() (time.Time, error) {
 
 // save timestamp, if lastTs is 0, we think the timestamp doesn't exist, so create it,
 // otherwise, update it.
-func (s *Server) saveTimestamp(now time.Time) error {
-	data := uint64ToBytes(uint64(now.UnixNano()))
+func (s *Server) saveTimestamp(ts time.Time) error {
+	data := uint64ToBytes(uint64(ts.UnixNano()))
 	key := s.getTimestampPath()
 
 	resp, err := s.leaderTxn().Then(clientv3.OpPut(key, string(data))).Commit()
@@ -69,7 +69,7 @@ func (s *Server) saveTimestamp(now time.Time) error {
 		return errors.New("save timestamp failed, maybe we lost leader")
 	}
 
-	s.lastSavedTime = now
+	s.lastSavedTime = ts
 
 	return nil
 }
@@ -82,69 +82,88 @@ func (s *Server) syncTimestamp() error {
 		return errors.Trace(err)
 	}
 
-	var now time.Time
-
-	for {
-		now = time.Now()
-		if wait := subTimeByWallClock(last, now) + updateTimestampGuard; wait > 0 {
-			tsoCounter.WithLabelValues("sync_wait").Inc()
-			log.Warnf("wait %v to guarantee valid generated timestamp", wait)
-			time.Sleep(wait)
-			continue
-		}
-		break
+	next := time.Now()
+	// If the current system time minus the saved etcd timestamp is less than `updateTimestampGuard`,
+	// the timestamp allocation will start from the saved etcd timestamp temporarily.
+	if subTimeByWallClock(next, last) < updateTimestampGuard {
+		log.Errorf("system time may be incorrect: last: %v next %v", last, next)
+		next = last.Add(updateTimestampGuard)
 	}
 
-	save := now.Add(s.cfg.TsoSaveInterval.Duration)
+	save := next.Add(s.cfg.TsoSaveInterval.Duration)
 	if err = s.saveTimestamp(save); err != nil {
 		return errors.Trace(err)
 	}
 
 	tsoCounter.WithLabelValues("sync_ok").Inc()
-	log.Infof("sync and save timestamp: last %v save %v", last, save)
+	log.Infof("sync and save timestamp: last %v save %v next %v", last, save, next)
 
 	current := &atomicObject{
-		physical: now,
+		physical: next,
 	}
 	s.ts.Store(current)
 
 	return nil
 }
 
+// This function will do two things:
+// 1. When the logical time is going to be used up, the current physical time needs to increase.
+// 2. If the time window is not enough, which means the saved etcd time minus the next physical time
+//    is less than or equal to `updateTimestampGuard`, it will need to be updated and save the
+//    next physical time plus `TsoSaveInterval` into etcd.
+//
+// Here is some constraints that this function must satisfy:
+// 1. The physical time is monotonically increasing.
+// 2. The saved time is monotonically increasing.
+// 3. The physical time is always less than the saved timestamp.
 func (s *Server) updateTimestamp() error {
-	prev := s.ts.Load().(*atomicObject).physical
+	prev := s.ts.Load().(*atomicObject)
 	now := time.Now()
 
 	tsoCounter.WithLabelValues("save").Inc()
 
-	since := subTimeByWallClock(now, prev)
-	if since > 3*updateTimestampStep {
-		log.Warnf("clock offset: %v, prev: %v, now: %v", since, prev, now)
+	jetLag := subTimeByWallClock(now, prev.physical)
+	if jetLag > 3*updateTimestampStep {
+		log.Warnf("clock offset: %v, prev: %v, now: %v", jetLag, prev.physical, now)
 		tsoCounter.WithLabelValues("slow_save").Inc()
 	}
-	// Avoid the same physical time stamp
-	if since <= updateTimestampGuard {
+
+	if jetLag < 0 {
+		tsoCounter.WithLabelValues("system_time_slow").Inc()
+	}
+
+	var next time.Time
+	prevLogical := atomic.LoadInt64(&prev.logical)
+	// If the system time is greater, it will be synchronized with the system time.
+	if jetLag > updateTimestampGuard {
+		next = now
+	} else if prevLogical > maxLogical/2 {
+		// The reason choosing maxLogical/2 here is that it's big enough for common cases.
+		// Because there is enough timestamp can be allocated before next update.
+		log.Warnf("the logical time may be not enough, prevLogical: %v", prevLogical)
+		next = prev.physical.Add(time.Millisecond)
+	} else {
+		// It will still use the previous physical time to alloc the timestamp.
 		tsoCounter.WithLabelValues("skip_save").Inc()
-		log.Warnf("invalid physical timestamp, prev: %v, now: %v, re-update later", prev, now)
 		return nil
 	}
 
-	if subTimeByWallClock(now, s.lastSavedTime) >= 0 {
-		last := s.lastSavedTime
-		save := now.Add(s.cfg.TsoSaveInterval.Duration)
+	// It is not safe to increase the physical time to `next`.
+	// The time window needs to be updated and saved to etcd.
+	if subTimeByWallClock(s.lastSavedTime, next) <= updateTimestampGuard {
+		save := next.Add(s.cfg.TsoSaveInterval.Duration)
 		if err := s.saveTimestamp(save); err != nil {
 			return errors.Trace(err)
 		}
-
-		tsoCounter.WithLabelValues("save_ok").Inc()
-		log.Debugf("save timestamp ok: prev %v last %v save %v", prev, last, save)
 	}
 
 	current := &atomicObject{
-		physical: now,
+		physical: next,
+		logical:  0,
 	}
+
 	s.ts.Store(current)
-	metadataGauge.WithLabelValues("tso").Set(float64(now.Unix()))
+	metadataGauge.WithLabelValues("tso").Set(float64(next.Unix()))
 
 	return nil
 }
@@ -165,6 +184,7 @@ func (s *Server) getRespTS(count uint32) (pdpb.Timestamp, error) {
 		resp.Logical = atomic.AddInt64(&current.logical, int64(count))
 		if resp.Logical >= maxLogical {
 			log.Errorf("logical part outside of max logical interval %v, please check ntp time, retry count %d", resp, i)
+			tsoCounter.WithLabelValues("logical_overflow").Inc()
 			time.Sleep(updateTimestampStep)
 			continue
 		}