diff --git a/doc/source/whatsnew/v2.1.0.rst b/doc/source/whatsnew/v2.1.0.rst
index 299adc5af8aea..1c0798e6cf9b1 100644
--- a/doc/source/whatsnew/v2.1.0.rst
+++ b/doc/source/whatsnew/v2.1.0.rst
@@ -425,6 +425,7 @@ Reshaping
 ^^^^^^^^^
 - Bug in :func:`crosstab` when ``dropna=False`` would not keep ``np.nan`` in the result (:issue:`10772`)
 - Bug in :meth:`DataFrame.agg` and :meth:`Series.agg` on non-unique columns would return incorrect type when dist-like argument passed in (:issue:`51099`)
+- Bug in :meth:`DataFrame.merge` not merging correctly when having ``MultiIndex`` with single level (:issue:`52331`)
 - Bug in :meth:`DataFrame.stack` losing extension dtypes when columns is a :class:`MultiIndex` and frame contains mixed dtypes (:issue:`45740`)
 - Bug in :meth:`DataFrame.transpose` inferring dtype for object column (:issue:`51546`)
 - Bug in :meth:`Series.combine_first` converting ``int64`` dtype to ``float64`` and losing precision on very large integers (:issue:`51764`)
diff --git a/pandas/core/reshape/merge.py b/pandas/core/reshape/merge.py
index 7c046bddab4e8..7316e29b0ce40 100644
--- a/pandas/core/reshape/merge.py
+++ b/pandas/core/reshape/merge.py
@@ -2267,23 +2267,14 @@ def _get_no_sort_one_missing_indexer(
 def _left_join_on_index(
     left_ax: Index, right_ax: Index, join_keys, sort: bool = False
 ) -> tuple[Index, npt.NDArray[np.intp] | None, npt.NDArray[np.intp]]:
-    if len(join_keys) > 1:
-        if not (
-            isinstance(right_ax, MultiIndex) and len(join_keys) == right_ax.nlevels
-        ):
-            raise AssertionError(
-                "If more than one join key is given then "
-                "'right_ax' must be a MultiIndex and the "
-                "number of join keys must be the number of levels in right_ax"
-            )
-
+    if isinstance(right_ax, MultiIndex):
         left_indexer, right_indexer = _get_multiindex_indexer(
             join_keys, right_ax, sort=sort
         )
     else:
-        jkey = join_keys[0]
-
-        left_indexer, right_indexer = _get_single_indexer(jkey, right_ax, sort=sort)
+        left_indexer, right_indexer = _get_single_indexer(
+            join_keys[0], right_ax, sort=sort
+        )
 
     if sort or len(left_ax) != len(left_indexer):
         # if asked to sort or there are 1-to-many matches
diff --git a/pandas/tests/reshape/merge/test_merge.py b/pandas/tests/reshape/merge/test_merge.py
index 088ebf6c88e6a..cb773a30901a2 100644
--- a/pandas/tests/reshape/merge/test_merge.py
+++ b/pandas/tests/reshape/merge/test_merge.py
@@ -2797,3 +2797,16 @@ def test_merge_datetime_different_resolution(tzinfo):
     )
     result = df1.merge(df2, on="t")
     tm.assert_frame_equal(result, expected)
+
+
+def test_merge_multiindex_single_level():
+    # GH #52331
+    df = DataFrame({"col": ["A", "B"]})
+    df2 = DataFrame(
+        data={"b": [100]},
+        index=MultiIndex.from_tuples([("A",), ("C",)], names=["col"]),
+    )
+    expected = DataFrame({"col": ["A", "B"], "b": [100, np.nan]})
+
+    result = df.merge(df2, left_on=["col"], right_index=True, how="left")
+    tm.assert_frame_equal(result, expected)