5,6-Difluorobenzo[c] [1,2,5]thiadiazole (FBT)-based conjugated donor-acceptor (D-A) polymers with straight and branched side chains were synthesized via Stille-coupling copolymerization to study their physical, optoelectronic and photovoltaic properties. The results show that both the nature of pendant side chains and the electron acceptor strength of the acceptor moiety of D-A polymers have critical impacts on material and photovoltaic properties. Better pi-pi stacking of polymer backbones enabled by appropriate substituents such as fluorine atoms and branched alkyl chains leads to a reasonably high power conversion efficiency of over 6% when the polymer is utilized as a donor material with PC71BM as an active layer in bulk heterojunction solar cells.