diff --git a/br/pkg/lightning/restore/check_info_test.go b/br/pkg/lightning/restore/check_info_test.go
index 3a8a666699164..36903ab93b22c 100644
--- a/br/pkg/lightning/restore/check_info_test.go
+++ b/br/pkg/lightning/restore/check_info_test.go
@@ -493,11 +493,11 @@ func TestCheckTableEmpty(t *testing.T) {
 	require.NoError(t, err)
 	mock.MatchExpectationsInOrder(false)
 	targetInfoGetter.targetDBGlue = glue.NewExternalTiDBGlue(db, mysql.ModeNone)
-	mock.ExpectQuery("SELECT 1 FROM `test1`.`tbl1` LIMIT 1").
+	mock.ExpectQuery("SELECT 1 FROM `test1`.`tbl1` USE INDEX\\(\\) LIMIT 1").
 		WillReturnRows(sqlmock.NewRows([]string{""}).RowError(0, sql.ErrNoRows))
-	mock.ExpectQuery("SELECT 1 FROM `test1`.`tbl2` LIMIT 1").
+	mock.ExpectQuery("SELECT 1 FROM `test1`.`tbl2` USE INDEX\\(\\) LIMIT 1").
 		WillReturnRows(sqlmock.NewRows([]string{""}).RowError(0, sql.ErrNoRows))
-	mock.ExpectQuery("SELECT 1 FROM `test2`.`tbl1` LIMIT 1").
+	mock.ExpectQuery("SELECT 1 FROM `test2`.`tbl1` USE INDEX\\(\\) LIMIT 1").
 		WillReturnRows(sqlmock.NewRows([]string{""}).RowError(0, sql.ErrNoRows))
 	rc.checkTemplate = NewSimpleTemplate()
 	err = rc.checkTableEmpty(ctx)
@@ -510,13 +510,13 @@ func TestCheckTableEmpty(t *testing.T) {
 	targetInfoGetter.targetDBGlue = glue.NewExternalTiDBGlue(db, mysql.ModeNone)
 	mock.MatchExpectationsInOrder(false)
 	// test auto retry retryable error
-	mock.ExpectQuery("SELECT 1 FROM `test1`.`tbl1` LIMIT 1").
+	mock.ExpectQuery("SELECT 1 FROM `test1`.`tbl1` USE INDEX\\(\\) LIMIT 1").
 		WillReturnError(&gmysql.MySQLError{Number: errno.ErrPDServerTimeout})
-	mock.ExpectQuery("SELECT 1 FROM `test1`.`tbl1` LIMIT 1").
+	mock.ExpectQuery("SELECT 1 FROM `test1`.`tbl1` USE INDEX\\(\\) LIMIT 1").
 		WillReturnRows(sqlmock.NewRows([]string{""}).RowError(0, sql.ErrNoRows))
-	mock.ExpectQuery("SELECT 1 FROM `test1`.`tbl2` LIMIT 1").
+	mock.ExpectQuery("SELECT 1 FROM `test1`.`tbl2` USE INDEX\\(\\) LIMIT 1").
 		WillReturnRows(sqlmock.NewRows([]string{""}).RowError(0, sql.ErrNoRows))
-	mock.ExpectQuery("SELECT 1 FROM `test2`.`tbl1` LIMIT 1").
+	mock.ExpectQuery("SELECT 1 FROM `test2`.`tbl1` USE INDEX\\(\\) LIMIT 1").
 		WillReturnRows(sqlmock.NewRows([]string{""}).AddRow(1))
 	rc.checkTemplate = NewSimpleTemplate()
 	err = rc.checkTableEmpty(ctx)
@@ -532,11 +532,11 @@ func TestCheckTableEmpty(t *testing.T) {
 	require.NoError(t, err)
 	targetInfoGetter.targetDBGlue = glue.NewExternalTiDBGlue(db, mysql.ModeNone)
 	mock.MatchExpectationsInOrder(false)
-	mock.ExpectQuery("SELECT 1 FROM `test1`.`tbl1` LIMIT 1").
+	mock.ExpectQuery("SELECT 1 FROM `test1`.`tbl1` USE INDEX\\(\\) LIMIT 1").
 		WillReturnRows(sqlmock.NewRows([]string{""}).AddRow(1))
-	mock.ExpectQuery("SELECT 1 FROM `test1`.`tbl2` LIMIT 1").
+	mock.ExpectQuery("SELECT 1 FROM `test1`.`tbl2` USE INDEX\\(\\) LIMIT 1").
 		WillReturnRows(sqlmock.NewRows([]string{""}).RowError(0, sql.ErrNoRows))
-	mock.ExpectQuery("SELECT 1 FROM `test2`.`tbl1` LIMIT 1").
+	mock.ExpectQuery("SELECT 1 FROM `test2`.`tbl1` USE INDEX\\(\\) LIMIT 1").
 		WillReturnRows(sqlmock.NewRows([]string{""}).AddRow(1))
 	rc.checkTemplate = NewSimpleTemplate()
 	err = rc.checkTableEmpty(ctx)
@@ -576,7 +576,7 @@ func TestCheckTableEmpty(t *testing.T) {
 	require.NoError(t, err)
 	targetInfoGetter.targetDBGlue = glue.NewExternalTiDBGlue(db, mysql.ModeNone)
 	// only need to check the one that is not in checkpoint
-	mock.ExpectQuery("SELECT 1 FROM `test1`.`tbl2` LIMIT 1").
+	mock.ExpectQuery("SELECT 1 FROM `test1`.`tbl2` USE INDEX\\(\\) LIMIT 1").
 		WillReturnRows(sqlmock.NewRows([]string{""}).RowError(0, sql.ErrNoRows))
 	err = rc.checkTableEmpty(ctx)
 	require.NoError(t, err)
diff --git a/br/pkg/lightning/restore/get_pre_info.go b/br/pkg/lightning/restore/get_pre_info.go
index 93927c6956809..4273ff708a89b 100644
--- a/br/pkg/lightning/restore/get_pre_info.go
+++ b/br/pkg/lightning/restore/get_pre_info.go
@@ -189,7 +189,12 @@ func (g *TargetInfoGetterImpl) IsTableEmpty(ctx context.Context, schemaName stri
 	}
 	var dump int
 	err = exec.QueryRow(ctx, "check table empty",
-		fmt.Sprintf("SELECT 1 FROM %s LIMIT 1", common.UniqueTable(schemaName, tableName)),
+		// Here we use the `USE INDEX()` hint to skip fetch the record from index.
+		// In Lightning, if previous importing is halted half-way, it is possible that
+		// the data is partially imported, but the index data has not been imported.
+		// In this situation, if no hint is added, the SQL executor might fetch the record from index,
+		// which is empty.  This will result in missing check.
+		fmt.Sprintf("SELECT 1 FROM %s USE INDEX() LIMIT 1", common.UniqueTable(schemaName, tableName)),
 		&dump,
 	)
 
diff --git a/br/pkg/lightning/restore/get_pre_info_test.go b/br/pkg/lightning/restore/get_pre_info_test.go
index f66a76901116f..71c2810d0b60e 100644
--- a/br/pkg/lightning/restore/get_pre_info_test.go
+++ b/br/pkg/lightning/restore/get_pre_info_test.go
@@ -762,7 +762,7 @@ func TestGetPreInfoIsTableEmpty(t *testing.T) {
 	require.NoError(t, err)
 	require.Equal(t, lnConfig, targetGetter.cfg)
 
-	mock.ExpectQuery("SELECT 1 FROM `test_db`.`test_tbl` LIMIT 1").
+	mock.ExpectQuery("SELECT 1 FROM `test_db`.`test_tbl` USE INDEX\\(\\) LIMIT 1").
 		WillReturnError(&mysql_sql_driver.MySQLError{
 			Number:  errno.ErrNoSuchTable,
 			Message: "Table 'test_db.test_tbl' doesn't exist",
@@ -772,7 +772,7 @@ func TestGetPreInfoIsTableEmpty(t *testing.T) {
 	require.NotNil(t, pIsEmpty)
 	require.Equal(t, true, *pIsEmpty)
 
-	mock.ExpectQuery("SELECT 1 FROM `test_db`.`test_tbl` LIMIT 1").
+	mock.ExpectQuery("SELECT 1 FROM `test_db`.`test_tbl` USE INDEX\\(\\) LIMIT 1").
 		WillReturnRows(
 			sqlmock.NewRows([]string{"1"}).
 				RowError(0, sql.ErrNoRows),
@@ -782,7 +782,7 @@ func TestGetPreInfoIsTableEmpty(t *testing.T) {
 	require.NotNil(t, pIsEmpty)
 	require.Equal(t, true, *pIsEmpty)
 
-	mock.ExpectQuery("SELECT 1 FROM `test_db`.`test_tbl` LIMIT 1").
+	mock.ExpectQuery("SELECT 1 FROM `test_db`.`test_tbl` USE INDEX\\(\\) LIMIT 1").
 		WillReturnRows(
 			sqlmock.NewRows([]string{"1"}).AddRow(1),
 		)
@@ -791,7 +791,7 @@ func TestGetPreInfoIsTableEmpty(t *testing.T) {
 	require.NotNil(t, pIsEmpty)
 	require.Equal(t, false, *pIsEmpty)
 
-	mock.ExpectQuery("SELECT 1 FROM `test_db`.`test_tbl` LIMIT 1").
+	mock.ExpectQuery("SELECT 1 FROM `test_db`.`test_tbl` USE INDEX\\(\\) LIMIT 1").
 		WillReturnError(errors.New("some dummy error"))
 	_, err = targetGetter.IsTableEmpty(ctx, "test_db", "test_tbl")
 	require.Error(t, err)
diff --git a/br/pkg/lightning/restore/table_restore.go b/br/pkg/lightning/restore/table_restore.go
index c1556e36b0824..86d3ed2622ddc 100644
--- a/br/pkg/lightning/restore/table_restore.go
+++ b/br/pkg/lightning/restore/table_restore.go
@@ -384,6 +384,11 @@ func (tr *TableRestore) restoreEngines(pCtx context.Context, rc *Controller, cp
 	if cp.Status < checkpoints.CheckpointStatusIndexImported {
 		var err error
 		if indexEngineCp.Status < checkpoints.CheckpointStatusImported {
+			failpoint.Inject("FailBeforeStartImportingIndexEngine", func() {
+				errMsg := "fail before importing index KV data"
+				tr.logger.Warn(errMsg)
+				failpoint.Return(errors.New(errMsg))
+			})
 			err = tr.importKV(ctx, closedIndexEngine, rc, indexEngineID)
 			failpoint.Inject("FailBeforeIndexEngineImported", func() {
 				finished := rc.status.FinishedFileSize.Load()
diff --git a/br/tests/lightning_check_partial_imported/config.toml b/br/tests/lightning_check_partial_imported/config.toml
new file mode 100644
index 0000000000000..30cb6fe6b4eb3
--- /dev/null
+++ b/br/tests/lightning_check_partial_imported/config.toml
@@ -0,0 +1,5 @@
+[tikv-importer]
+backend = "local"
+
+[mydumper.csv]
+header = true
diff --git a/br/tests/lightning_check_partial_imported/data/db01.tbl01-schema.sql b/br/tests/lightning_check_partial_imported/data/db01.tbl01-schema.sql
new file mode 100644
index 0000000000000..b6832e95d95e3
--- /dev/null
+++ b/br/tests/lightning_check_partial_imported/data/db01.tbl01-schema.sql
@@ -0,0 +1,12 @@
+CREATE TABLE tbl01 (
+  `id` INTEGER,
+  `val` VARCHAR(64),
+  `aaa` CHAR(66) DEFAULT NULL,
+  `bbb` CHAR(10) NOT NULL,
+  `ccc` CHAR(42) DEFAULT NULL,
+  `ddd` CHAR(42) DEFAULT NULL,
+  `eee` CHAR(66) DEFAULT NULL,
+  `fff` VARCHAR(128) DEFAULT NULL,
+  KEY `aaa` (`aaa`),
+  PRIMARY KEY (`id`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_bin;
diff --git a/br/tests/lightning_check_partial_imported/data/db01.tbl01.csv b/br/tests/lightning_check_partial_imported/data/db01.tbl01.csv
new file mode 100644
index 0000000000000..108134af2ee72
--- /dev/null
+++ b/br/tests/lightning_check_partial_imported/data/db01.tbl01.csv
@@ -0,0 +1,6 @@
+id,val,aaa,bbb,ccc,ddd,eee,fff
+1,"v01","a01","b01","c01","d01","e01","f01"
+2,"v02","a02","b02","c02","d02","e02","f02"
+3,"v03","a03","b03","c03","d03","e03","f03"
+4,"v04","a04","b04","c04","d04","e04","f04"
+5,"v05","a05","b05","c05","d05","e05","f05"
diff --git a/br/tests/lightning_check_partial_imported/run.sh b/br/tests/lightning_check_partial_imported/run.sh
new file mode 100755
index 0000000000000..00ed78a5013d1
--- /dev/null
+++ b/br/tests/lightning_check_partial_imported/run.sh
@@ -0,0 +1,47 @@
+#!/bin/bash
+#
+# Copyright 2022 PingCAP, Inc.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+MYDIR=$(dirname "${BASH_SOURCE[0]}")
+set -eux
+
+check_cluster_version 4 0 0 'local backend' || exit 0
+
+export GO_FAILPOINTS="github.com/pingcap/tidb/br/pkg/lightning/restore/FailBeforeStartImportingIndexEngine=return"
+set +e
+if run_lightning; then
+    echo "The first import doesn't fail as expected" >&2
+    exit 1
+fi
+set -e
+
+data_records=$(tail -n +2 "${MYDIR}/data/db01.tbl01.csv" | wc -l | xargs echo )
+run_sql "SELECT COUNT(*) FROM db01.tbl01 USE INDEX();"
+check_contains "${data_records}"
+
+export GO_FAILPOINTS=""
+set +e
+if run_lightning --check-requirements=1; then
+    echo "The pre-check doesn't find out the non-empty table problem"
+    exit 2
+fi
+set -e
+
+run_sql "TRUNCATE TABLE db01.tbl01;"
+run_lightning --check-requirements=1
+run_sql "SELECT COUNT(*) FROM db01.tbl01;"
+check_contains "${data_records}"
+run_sql "SELECT COUNT(*) FROM db01.tbl01 USE INDEX();"
+check_contains "${data_records}"