diff --git a/src/query/src/query_engine/state.rs b/src/query/src/query_engine/state.rs
index ab63c6491a..54c6b85c7a 100644
--- a/src/query/src/query_engine/state.rs
+++ b/src/query/src/query_engine/state.rs
@@ -90,7 +90,15 @@ impl QueryEngineState {
         plugins: Plugins,
     ) -> Self {
         let runtime_env = Arc::new(RuntimeEnv::default());
-        let session_config = SessionConfig::new().with_create_default_catalog_and_schema(false);
+        let mut session_config = SessionConfig::new().with_create_default_catalog_and_schema(false);
+
+        // todo(hl): This serves as a workaround for https://github.com/GreptimeTeam/greptimedb/issues/5659
+        // and we can add that check back once we upgrade datafusion.
+        session_config
+            .options_mut()
+            .execution
+            .skip_physical_aggregate_schema_check = true;
+
         // Apply extension rules
         let mut extension_rules = Vec::new();
 
diff --git a/tests/cases/standalone/common/cte/cte.result b/tests/cases/standalone/common/cte/cte.result
index c63ae6735f..48b0dfd4f1 100644
--- a/tests/cases/standalone/common/cte/cte.result
+++ b/tests/cases/standalone/common/cte/cte.result
@@ -130,3 +130,42 @@ drop table a;
 
 Affected Rows: 0
 
+CREATE TABLE grpc_latencies
+(
+    ts      TIMESTAMP TIME INDEX,
+    host    VARCHAR(255),
+    latency FLOAT,
+    PRIMARY KEY (host),
+);
+
+Affected Rows: 0
+
+INSERT INTO grpc_latencies
+VALUES ('2023-10-01 10:00:00', 'host1', 120),
+       ('2023-10-01 10:00:00', 'host2', 150),
+       ('2023-10-01 10:00:05', 'host1', 130);
+
+Affected Rows: 3
+
+WITH latencies AS (SELECT ts,
+                          host,
+                          AVG(latency) RANGE '2s' AS avg_latency
+                   FROM grpc_latencies ALIGN '2s' BY (host) FILL PREV
+    )
+SELECT latencies.ts,
+       AVG(latencies.avg_latency)
+FROM latencies
+GROUP BY latencies.ts ORDER BY latencies.ts;
+
++---------------------+----------------------------+
+| ts                  | avg(latencies.avg_latency) |
++---------------------+----------------------------+
+| 2023-10-01T10:00:00 | 135.0                      |
+| 2023-10-01T10:00:02 | 120.0                      |
+| 2023-10-01T10:00:04 | 130.0                      |
++---------------------+----------------------------+
+
+DROP TABLE grpc_latencies;
+
+Affected Rows: 0
+
diff --git a/tests/cases/standalone/common/cte/cte.sql b/tests/cases/standalone/common/cte/cte.sql
index 0b190df11f..b3eda58fb5 100644
--- a/tests/cases/standalone/common/cte/cte.sql
+++ b/tests/cases/standalone/common/cte/cte.sql
@@ -49,3 +49,30 @@ from cte
 where alias2 > 0;
 
 drop table a;
+
+
+CREATE TABLE grpc_latencies
+(
+    ts      TIMESTAMP TIME INDEX,
+    host    VARCHAR(255),
+    latency FLOAT,
+    PRIMARY KEY (host),
+);
+
+INSERT INTO grpc_latencies
+VALUES ('2023-10-01 10:00:00', 'host1', 120),
+       ('2023-10-01 10:00:00', 'host2', 150),
+       ('2023-10-01 10:00:05', 'host1', 130);
+
+
+WITH latencies AS (SELECT ts,
+                          host,
+                          AVG(latency) RANGE '2s' AS avg_latency
+                   FROM grpc_latencies ALIGN '2s' BY (host) FILL PREV
+    )
+SELECT latencies.ts,
+       AVG(latencies.avg_latency)
+FROM latencies
+GROUP BY latencies.ts ORDER BY latencies.ts;
+
+DROP TABLE grpc_latencies;