diff --git a/doc/source/whatsnew/v2.0.0.rst b/doc/source/whatsnew/v2.0.0.rst
index c2abb70988dad..5f7d2af92e839 100644
--- a/doc/source/whatsnew/v2.0.0.rst
+++ b/doc/source/whatsnew/v2.0.0.rst
@@ -568,6 +568,7 @@ MultiIndex
 - Bug in :meth:`MultiIndex.union` not sorting when sort=None and index contains missing values (:issue:`49010`)
 - Bug in :meth:`MultiIndex.append` not checking names for equality (:issue:`48288`)
 - Bug in :meth:`MultiIndex.symmetric_difference` losing extension array (:issue:`48607`)
+- Bug in :meth:`MultiIndex.value_counts` returning a :class:`Series` indexed by flat index of tuples instead of a :class:`MultiIndex` (:issue:`49558`)
 -
 
 I/O
diff --git a/pandas/core/algorithms.py b/pandas/core/algorithms.py
index 7494a8a54f9bb..7be5e4e33bf3a 100644
--- a/pandas/core/algorithms.py
+++ b/pandas/core/algorithms.py
@@ -871,6 +871,14 @@ def value_counts(
             result.name = name
             counts = result._values
 
+        elif isinstance(values, ABCMultiIndex):
+            # GH49558
+            levels = list(range(values.nlevels))
+            result = Series(index=values).groupby(level=levels, dropna=dropna).size()
+            # TODO: allow index names to remain (see discussion in GH49497)
+            result.index.names = [None] * values.nlevels
+            counts = result._values
+
         else:
             values = _ensure_arraylike(values)
             keys, counts = value_counts_arraylike(values, dropna)
diff --git a/pandas/tests/base/test_value_counts.py b/pandas/tests/base/test_value_counts.py
index f6ad3f24434d3..dafbd9fee1b8e 100644
--- a/pandas/tests/base/test_value_counts.py
+++ b/pandas/tests/base/test_value_counts.py
@@ -29,8 +29,6 @@ def test_value_counts(index_or_series_obj):
     counter = collections.Counter(obj)
     expected = Series(dict(counter.most_common()), dtype=np.int64, name=obj.name)
     expected.index = expected.index.astype(obj.dtype)
-    if isinstance(obj, pd.MultiIndex):
-        expected.index = Index(expected.index)
 
     if not isinstance(result.dtype, np.dtype):
         # i.e IntegerDtype