A series of conjugated polymers using naphtho[1,2-c: 5,6-c]bis[1,2,5]thiadiazole and benzodithiophene alternating backbone is synthesized to investigate the effect of side chain substitution on conjugated donor-acceptor polymer on electronic, morphological, and photovoltaic properties. It is found that light absorption and frontier energy levels of the resultant polymers are strongly affected by the side chains. The thin film morphology, crystal structure, crystallinity, and orientation also depend on the side chains; the side chain type affects more in the pi-pi stacking direction, while the side chain density plays a significant role in the lamellar packing direction. The thickness of the active layer also influences the performance of the solar cells with some materials showing enhanced performance with thicker active layers. The best solar cell device in this study has power conversion efficiencies of 8.14%, among the highest in materials of similar structure.