Pandas – GroupBy and then Merge on original table

By default, groupby output has the grouping columns as indicies, not columns, which is why the merge is failing.

There are a couple different ways to handle it, probably the easiest is using the as_index parameter when you define the groupby object.

po_grouped_df = poagg_df.groupby(['EID','PCODE'], as_index=False)

Then, your merge should work as expected.

In [356]: pd.merge(acc_df, pol_df, on=['EID','PCODE'], how='inner',suffixes=('_Acc','_Po'))
Out[356]: 
   EID PCODE  SC_Acc  EE_Acc        SI_Acc  PVALUE_Acc  EE_Po  PVALUE_Po  \
0  123    GR     236   40000  1.805222e+31         350  10000         50   
1  123    GR     236   40000  1.805222e+31         350  30000        300   
2  123    GU     443   12000  8.765549e+87         250  10000        100   
3  123    GU     443   12000  8.765549e+87         250   2000        150   

   SC_Po  SI_Po  
0     23     40  
1    213    140  
2    230    400  
3    213    140