diff --git a/modin/config/envvars.py b/modin/config/envvars.py
index 92813a4165a..3f4f1f8ea19 100644
--- a/modin/config/envvars.py
+++ b/modin/config/envvars.py
@@ -644,8 +644,6 @@ def put(cls, value: int) -> None:
         if value <= 0:
             raise ValueError(f"Min partition size should be > 0, passed value {value}")
         super().put(value)
-        MinRowPartitionSize.put(value)
-        MinColumnPartitionSize.put(value)
 
     @classmethod
     def get(cls) -> int:
@@ -660,7 +658,8 @@ def get(cls) -> int:
 
         ErrorMessage.single_warning(
             "`MinPartitionSize` is deprecated and will be removed in a future version. "
-            + "Use `MinRowPartitionSize` and `MinColumnPartitionSize` instead.",
+            + "This config has no longer effect, "
+            + "use `MinRowPartitionSize` and `MinColumnPartitionSize` instead.",
             FutureWarning,
         )
         min_partition_size = super().get()