diff --git a/pkg/domain/domain.go b/pkg/domain/domain.go
index 99bf7c4d86b31..11cb020eb340b 100644
--- a/pkg/domain/domain.go
+++ b/pkg/domain/domain.go
@@ -2293,6 +2293,25 @@ func (do *Domain) UpdateTableStatsLoop(ctx, initStatsCtx sessionctx.Context) err
 		},
 		"gcAnalyzeHistory",
 	)
+	do.wg.Run(
+		func() {
+			// The initStatsCtx is used to store the internal session for initializing stats,
+			// so we need the gc min start ts calculation to track it as an internal session.
+			// Since the session manager may not be ready at this moment, `infosync.StoreInternalSession` can fail.
+			// we need to retry until the session manager is ready or the init stats completes.
+			for !infosync.StoreInternalSession(initStatsCtx) {
+				waitRetry := time.After(time.Second)
+				select {
+				case <-do.StatsHandle().InitStatsDone:
+					return
+				case <-waitRetry:
+				}
+			}
+			<-do.StatsHandle().InitStatsDone
+			infosync.DeleteInternalSession(initStatsCtx)
+		},
+		"RemoveInitStatsFromInternalSessions",
+	)
 	return nil
 }
 
diff --git a/pkg/domain/infosync/info.go b/pkg/domain/infosync/info.go
index 5c4ee1889d58a..ed054cbb8bd7b 100644
--- a/pkg/domain/infosync/info.go
+++ b/pkg/domain/infosync/info.go
@@ -1283,16 +1283,22 @@ func ConfigureTiFlashPDForPartitions(accel bool, definitions *[]model.PartitionD
 }
 
 // StoreInternalSession is the entry function for store an internal session to SessionManager.
+<<<<<<< HEAD
 func StoreInternalSession(se interface{}) {
+=======
+// return whether the session is stored successfully.
+func StoreInternalSession(se any) bool {
+>>>>>>> bf704fd635c (domain: make the transaction from `initStatsCtx` blocking gc (#53602))
 	is, err := getGlobalInfoSyncer()
 	if err != nil {
-		return
+		return false
 	}
 	sm := is.GetSessionManager()
 	if sm == nil {
-		return
+		return false
 	}
 	sm.StoreInternalSession(se)
+	return true
 }
 
 // DeleteInternalSession is the entry function for delete an internal session from SessionManager.
diff --git a/pkg/server/BUILD.bazel b/pkg/server/BUILD.bazel
index 9a051f117b75e..cb54511209d19 100644
--- a/pkg/server/BUILD.bazel
+++ b/pkg/server/BUILD.bazel
@@ -186,6 +186,7 @@ go_test(
         "@com_github_prometheus_client_golang//prometheus/testutil",
         "@com_github_stretchr_testify//require",
         "@com_github_tikv_client_go_v2//error",
+        "@com_github_tikv_client_go_v2//oracle",
         "@com_github_tikv_client_go_v2//testutils",
         "@com_github_tikv_client_go_v2//tikv",
         "@org_uber_go_goleak//:goleak",
diff --git a/pkg/server/stat_test.go b/pkg/server/stat_test.go
index 31f7983cd000d..d0ffd2800685f 100644
--- a/pkg/server/stat_test.go
+++ b/pkg/server/stat_test.go
@@ -20,12 +20,14 @@ import (
 	"time"
 
 	"github.com/pingcap/failpoint"
+	"github.com/pingcap/tidb/pkg/config"
 	"github.com/pingcap/tidb/pkg/domain/infosync"
 	"github.com/pingcap/tidb/pkg/keyspace"
 	"github.com/pingcap/tidb/pkg/server/internal/util"
 	"github.com/pingcap/tidb/pkg/session"
 	"github.com/pingcap/tidb/pkg/store/mockstore"
 	"github.com/stretchr/testify/require"
+	"github.com/tikv/client-go/v2/oracle"
 )
 
 func TestUptime(t *testing.T) {
@@ -63,3 +65,46 @@ func TestUptime(t *testing.T) {
 	require.NoError(t, err)
 	require.GreaterOrEqual(t, stats[upTime].(int64), int64(time.Since(time.Unix(1282967700, 0)).Seconds()))
 }
+
+func TestInitStatsSessionBlockGC(t *testing.T) {
+	origConfig := config.GetGlobalConfig()
+	defer func() {
+		config.StoreGlobalConfig(origConfig)
+	}()
+	newConfig := *origConfig
+	for _, lite := range []bool{false, true} {
+		require.NoError(t, failpoint.Enable("github.com/pingcap/tidb/pkg/statistics/handle/beforeInitStats", "pause"))
+		require.NoError(t, failpoint.Enable("github.com/pingcap/tidb/pkg/statistics/handle/beforeInitStatsLite", "pause"))
+		newConfig.Performance.LiteInitStats = lite
+		config.StoreGlobalConfig(&newConfig)
+
+		store, err := mockstore.NewMockStore()
+		require.NoError(t, err)
+		dom, err := session.BootstrapSession(store)
+		require.NoError(t, err)
+
+		infoSyncer := dom.InfoSyncer()
+		sv := CreateMockServer(t, store)
+		sv.SetDomain(dom)
+		infoSyncer.SetSessionManager(sv)
+		time.Sleep(time.Second)
+		require.Eventually(t, func() bool {
+			now := time.Now()
+			startTSList := sv.GetInternalSessionStartTSList()
+			for _, startTs := range startTSList {
+				if startTs != 0 {
+					startTime := oracle.GetTimeFromTS(startTs)
+					// test pass if the min_start_ts is blocked over 1s.
+					if now.Sub(startTime) > time.Second {
+						return true
+					}
+				}
+			}
+			return false
+		}, 10*time.Second, 10*time.Millisecond, "min_start_ts is not blocked over 1s")
+		require.NoError(t, failpoint.Disable("github.com/pingcap/tidb/pkg/statistics/handle/beforeInitStats"))
+		require.NoError(t, failpoint.Disable("github.com/pingcap/tidb/pkg/statistics/handle/beforeInitStatsLite"))
+		dom.Close()
+		require.NoError(t, store.Close())
+	}
+}
diff --git a/pkg/statistics/handle/BUILD.bazel b/pkg/statistics/handle/BUILD.bazel
index 4ed865fdfaced..628e4b0cfef3a 100644
--- a/pkg/statistics/handle/BUILD.bazel
+++ b/pkg/statistics/handle/BUILD.bazel
@@ -40,9 +40,12 @@ go_library(
         "//pkg/util/logutil",
         "@com_github_pingcap_errors//:errors",
         "@com_github_pingcap_failpoint//:failpoint",
+<<<<<<< HEAD
         "@com_github_tiancaiamao_gp//:gp",
         "@org_golang_x_sync//singleflight",
         "@org_uber_go_atomic//:atomic",
+=======
+>>>>>>> bf704fd635c (domain: make the transaction from `initStatsCtx` blocking gc (#53602))
         "@org_uber_go_zap//:zap",
     ],
 )
diff --git a/pkg/statistics/handle/bootstrap.go b/pkg/statistics/handle/bootstrap.go
index abd0dc5d00d79..1cc5441298dda 100644
--- a/pkg/statistics/handle/bootstrap.go
+++ b/pkg/statistics/handle/bootstrap.go
@@ -21,6 +21,7 @@ import (
 	"time"
 
 	"github.com/pingcap/errors"
+	"github.com/pingcap/failpoint"
 	"github.com/pingcap/tidb/pkg/config"
 	"github.com/pingcap/tidb/pkg/infoschema"
 	"github.com/pingcap/tidb/pkg/kv"
@@ -700,6 +701,7 @@ func (h *Handle) InitStatsLite(is infoschema.InfoSchema) (err error) {
 	if err != nil {
 		return err
 	}
+	failpoint.Inject("beforeInitStatsLite", func() {})
 	cache, err := h.initStatsMeta(is)
 	if err != nil {
 		return errors.Trace(err)
@@ -727,6 +729,7 @@ func (h *Handle) InitStats(is infoschema.InfoSchema) (err error) {
 	if err != nil {
 		return err
 	}
+	failpoint.Inject("beforeInitStats", func() {})
 	cache, err := h.initStatsMeta(is)
 	if err != nil {
 		return errors.Trace(err)