print (df)
one two three
0 1 1 10.0
1 1 1 40.0
2 1 1 NaN
3 1 2 NaN
4 1 2 20.0
5 1 2 NaN
6 1 3 NaN
7 1 3 NaN
df['three'] = df.groupby(['one','two'], sort=False)['three']
.apply(lambda x: x.fillna(x.mean()))
print (df)
one two three
0 1 1 10.0
1 1 1 40.0
2 1 1 25.0
3 1 2 20.0
4 1 2 20.0
5 1 2 20.0
6 1 3 NaN
7 1 3 NaN