We report effects of microwave-assisted polymerization on the photovoltaic performance of polymer solar cell using benzodithiophene-based polymer (PTB7) as a donor material. For systematic and comparative study, we synthesized PTB7 polymers through Stille-coupling polymerization under microwave conditions (M-PTB7, Mn = 75 kg mol-1, and D = 2.2) as well as thermal conditions (T-PTB7, Mn = 31 kg mol-1, D = 2.1). Although the microwave-assisted polymerization is a powerful method to increase the Mn of PTB7 without broadening D in a short time, this method decrease the power conversion efficiency from 7.8% (T-PTB7) to 2.8 % (MPTB7). We found that the microwave-assisted polymerization accelerates more structural defects from homo-coupling side reactions, resulting in a significant decrease in JSC and FF values for M-PTB7. The increased abundance of these homo-coupled units under the microwave-assisted conditions was demonstrated by various optical spectroscopy methods and the model reaction study.