diff --git a/executor/batch_point_get_test.go b/executor/batch_point_get_test.go
index 9bc170107b..4b1eda8abe 100644
--- a/executor/batch_point_get_test.go
+++ b/executor/batch_point_get_test.go
@@ -370,3 +370,32 @@ func TestPointGetForTemporaryTable(t *testing.T) {
 	tk.MustQuery("select * from t1 where id = 1").Check(testkit.Rows("1 1"))
 	tk.MustQuery("select * from t1 where id = 2").Check(testkit.Rows())
 }
+
+func TestBatchPointGetIssue46779(t *testing.T) {
+	store := testkit.CreateMockStore(t)
+
+	tk := testkit.NewTestKit(t, store)
+	tk.MustExec("use test")
+	tk.MustExec("drop table if exists t1")
+	tk.MustExec("CREATE TABLE t1 (id int, c varchar(128), primary key (id)) PARTITION BY HASH (id) PARTITIONS 3;")
+	tk.MustExec(`insert into t1 values (1, "a"), (11, "b"), (21, "c")`)
+	query := "select * from t1 where id in (1, 1, 11)"
+	require.True(t, tk.HasPlan(query, "Batch_Point_Get")) // check if BatchPointGet is used
+	tk.MustQuery(query).Sort().Check(testkit.Rows("1 a", "11 b"))
+	query = "select * from t1 where id in (1, 11, 11, 21)"
+	require.True(t, tk.HasPlan(query, "Batch_Point_Get")) // check if BatchPointGet is used
+	tk.MustQuery(query).Sort().Check(testkit.Rows("1 a", "11 b", "21 c"))
+
+	tk.MustExec("drop table if exists t2")
+	tk.MustExec(`CREATE TABLE t2 (id int, c varchar(128), primary key (id)) partition by range (id)(
+		partition p0 values less than (10), 
+		partition p1 values less than (20), 
+		partition p2 values less than (30));`)
+	tk.MustExec(`insert into t2 values (1, "a"), (11, "b"), (21, "c")`)
+	query = "select * from t2 where id in (1, 1, 11)"
+	require.True(t, tk.HasPlan(query, "Batch_Point_Get")) // check if BatchPointGet is used
+	tk.MustQuery(query).Sort().Check(testkit.Rows("1 a", "11 b"))
+	require.True(t, tk.HasPlan(query, "Batch_Point_Get")) // check if BatchPointGet is used
+	query = "select * from t2 where id in (1, 11, 11, 21)"
+	tk.MustQuery(query).Sort().Check(testkit.Rows("1 a", "11 b", "21 c"))
+}
diff --git a/executor/builder.go b/executor/builder.go
index 7fe26157b4..27166a2160 100644
--- a/executor/builder.go
+++ b/executor/builder.go
@@ -5226,16 +5226,22 @@ func (b *executorBuilder) buildBatchPointGet(plan *plannercore.BatchPointGetPlan
 		// `SELECT a FROM t WHERE a IN (1, 1, 2, 1, 2)` should not return duplicated rows
 		handles := make([]kv.Handle, 0, len(plan.Handles))
 		dedup := kv.NewHandleMap()
+		// Used for clear paritionIDs of duplicated rows.
+		dupPartPos := 0
 		if plan.IndexInfo == nil {
-			for _, handle := range plan.Handles {
+			for idx, handle := range plan.Handles {
 				if _, found := dedup.Get(handle); found {
 					continue
 				}
 				dedup.Set(handle, true)
 				handles = append(handles, handle)
+				if len(plan.PartitionIDs) > 0 {
+					e.planPhysIDs[dupPartPos] = e.planPhysIDs[idx]
+					dupPartPos++
+				}
 			}
 		} else {
-			for _, value := range plan.IndexValues {
+			for idx, value := range plan.IndexValues {
 				if datumsContainNull(value) {
 					continue
 				}
@@ -5257,9 +5263,16 @@ func (b *executorBuilder) buildBatchPointGet(plan *plannercore.BatchPointGetPlan
 				}
 				dedup.Set(handle, true)
 				handles = append(handles, handle)
+				if len(plan.PartitionIDs) > 0 {
+					e.planPhysIDs[dupPartPos] = e.planPhysIDs[idx]
+					dupPartPos++
+				}
 			}
 		}
 		e.handles = handles
+		if dupPartPos > 0 {
+			e.planPhysIDs = e.planPhysIDs[:dupPartPos]
+		}
 		capacity = len(e.handles)
 	}
 	e.Base().SetInitCap(capacity)