diff --git a/pkg/statistics/handle/storage/BUILD.bazel b/pkg/statistics/handle/storage/BUILD.bazel
index 5dffed12cb20f..72412b217a56d 100644
--- a/pkg/statistics/handle/storage/BUILD.bazel
+++ b/pkg/statistics/handle/storage/BUILD.bazel
@@ -59,7 +59,7 @@ go_test(
         "stats_read_writer_test.go",
     ],
     flaky = True,
-    shard_count = 23,
+    shard_count = 24,
     deps = [
         ":storage",
         "//pkg/domain",
@@ -76,6 +76,7 @@ go_test(
         "//pkg/testkit/analyzehelper",
         "//pkg/types",
         "//pkg/util",
+        "@com_github_pingcap_failpoint//:failpoint",
         "@com_github_stretchr_testify//require",
     ],
 )
diff --git a/pkg/statistics/handle/storage/gc.go b/pkg/statistics/handle/storage/gc.go
index 0d12327857952..9b42a224ff02e 100644
--- a/pkg/statistics/handle/storage/gc.go
+++ b/pkg/statistics/handle/storage/gc.go
@@ -22,6 +22,7 @@ import (
 	"time"
 
 	"github.com/pingcap/errors"
+	"github.com/pingcap/failpoint"
 	"github.com/pingcap/tidb/pkg/infoschema"
 	"github.com/pingcap/tidb/pkg/parser/terror"
 	"github.com/pingcap/tidb/pkg/sessionctx"
@@ -91,6 +92,10 @@ func GCStats(
 		return nil
 	}
 
+	failpoint.Inject("injectGCStatsLastTSOffset", func(val failpoint.Value) {
+		offset = uint64(val.(int))
+	})
+
 	// Get the last gc time.
 	gcVer := now - offset
 	lastGC, err := getLastGCTimestamp(sctx)
@@ -266,29 +271,36 @@ func removeDeletedExtendedStats(sctx sessionctx.Context, version uint64) (err er
 }
 
 // gcTableStats GC this table's stats.
+// The GC of a table will be a two-phase process:
+// 1. Delete the column/index's stats from storage. Then other TiDB nodes will be aware that those stats are deleted.
+// 2. Then delete the record in stats_meta.
 func gcTableStats(sctx sessionctx.Context,
 	statsHandler types.StatsHandle,
 	is infoschema.InfoSchema, physicalID int64) error {
+	tbl, ok := statsHandler.TableInfoByID(is, physicalID)
 	rows, _, err := util.ExecRows(sctx, "select is_index, hist_id from mysql.stats_histograms where table_id = %?", physicalID)
 	if err != nil {
 		return errors.Trace(err)
 	}
-	// The table has already been deleted in stats and acknowledged to all tidb,
-	// we can safely remove the meta info now.
-	if len(rows) == 0 {
+	if !ok {
+		if len(rows) > 0 {
+			// It's the first time to run into it. Delete column/index stats to notify other TiDB nodes.
+			logutil.BgLogger().Info("remove stats in GC due to dropped table", zap.Int64("tableID", physicalID))
+			return util.WrapTxn(sctx, func(sctx sessionctx.Context) error {
+				return errors.Trace(DeleteTableStatsFromKV(sctx, []int64{physicalID}))
+			})
+		}
+		// len(rows) == 0 => The table's stats is empty.
+		// The table has already been deleted in stats and acknowledged to all tidb,
+		// We can safely remove the meta info now.
 		_, _, err = util.ExecRows(sctx, "delete from mysql.stats_meta where table_id = %?", physicalID)
 		if err != nil {
 			return errors.Trace(err)
 		}
 		cache.TableRowStatsCache.Invalidate(physicalID)
+		return nil
 	}
-	tbl, ok := statsHandler.TableInfoByID(is, physicalID)
-	if !ok {
-		logutil.BgLogger().Info("remove stats in GC due to dropped table", zap.Int64("table_id", physicalID))
-		return util.WrapTxn(sctx, func(sctx sessionctx.Context) error {
-			return errors.Trace(DeleteTableStatsFromKV(sctx, []int64{physicalID}))
-		})
-	}
+
 	tblInfo := tbl.Meta()
 	for _, row := range rows {
 		isIndex, histID := row.GetInt64(0), row.GetInt64(1)
diff --git a/pkg/statistics/handle/storage/gc_test.go b/pkg/statistics/handle/storage/gc_test.go
index 42dd3d39a1137..3c480100e54fb 100644
--- a/pkg/statistics/handle/storage/gc_test.go
+++ b/pkg/statistics/handle/storage/gc_test.go
@@ -15,9 +15,12 @@
 package storage_test
 
 import (
+	"context"
 	"testing"
 	"time"
 
+	"github.com/pingcap/failpoint"
+	"github.com/pingcap/tidb/pkg/parser/model"
 	"github.com/pingcap/tidb/pkg/sessionctx/variable"
 	"github.com/pingcap/tidb/pkg/testkit"
 	"github.com/pingcap/tidb/pkg/testkit/analyzehelper"
@@ -174,3 +177,27 @@ func TestDeleteAnalyzeJobs(t *testing.T) {
 	rows = testKit.MustQuery("show analyze status").Rows()
 	require.Equal(t, 0, len(rows))
 }
+
+func TestExtremCaseOfGC(t *testing.T) {
+	// This case tests that there's no records in mysql.stats_histograms but this table is not deleted in fact.
+	// We should not delete the record in mysql.stats_meta.
+	store, dom := testkit.CreateMockStoreAndDomain(t)
+	testKit := testkit.NewTestKit(t, store)
+	testKit.MustExec("use test")
+	testKit.MustExec("create table t(a int, b int)")
+	testKit.MustExec("insert into t values (1,2),(3,4)")
+	testKit.MustExec("analyze table t")
+	tbl, err := dom.InfoSchema().TableByName(context.TODO(), model.NewCIStr("test"), model.NewCIStr("t"))
+	require.NoError(t, err)
+	tid := tbl.Meta().ID
+	rs := testKit.MustQuery("select * from mysql.stats_meta where table_id = ?", tid)
+	require.Len(t, rs.Rows(), 1)
+	rs = testKit.MustQuery("select * from mysql.stats_histograms where table_id = ?", tid)
+	require.Len(t, rs.Rows(), 0)
+	h := dom.StatsHandle()
+	failpoint.Enable("github.com/pingcap/tidb/pkg/statistics/handle/storage/injectGCStatsLastTSOffset", `return(0)`)
+	h.GCStats(dom.InfoSchema(), time.Second*3)
+	rs = testKit.MustQuery("select * from mysql.stats_meta where table_id = ?", tid)
+	require.Len(t, rs.Rows(), 1)
+	failpoint.Disable("github.com/pingcap/tidb/pkg/statistics/handle/storage/injectGCStatsLastTSOffset")
+}