Merge two dataframes with multi-index
Option 1
Use pd.DataFrame.reindex + pd.DataFrame.joinreindex has a convenient level parameter that allows you to expand on the index levels not present.
df1.join(df2.reindex(df1.index, level=0)) A B C D E Ffirst one a1 b1 c1 d1 e1 f1 two a2 b2 c2 d1 e1 f1second one a3 b3 c3 d2 e2 f2 two a4 b4 c4 d2 e2 f2Option 2
You can rename your axes and join will work
df1.rename_axis(['a', 'b']).join(df2.rename_axis('a')) A B C D E Fa b first one a1 b1 c1 d1 e1 f1 two a2 b2 c2 d1 e1 f1second one a3 b3 c3 d2 e2 f2 two a4 b4 c4 d2 e2 f2You can follow that up with another rename_axis to get desired results
df1.rename_axis(['a', 'b']).join(df2.rename_axis('a')).rename_axis([None, None]) A B C D E Ffirst one a1 b1 c1 d1 e1 f1 two a2 b2 c2 d1 e1 f1second one a3 b3 c3 d2 e2 f2 two a4 b4 c4 d2 e2 f2