Two new conjugated polymers based on the naphtho[2,3-c]thiophene-4,9-dione unit with different chemical structures but similar photoelectric properties were designed and synthesized. The differences and the related issues in their photovoltaic properties were well studied. The results show that both polymers can work well with PC71BM, recording PCEs of 7.2% for PBDT-DTN and 4.9% for PIDT-DTN. However, when blended with ITIC, PBDT-DTN can get a PCE of 8.3% compared with that of 1.1% for PLDT-DTN. It was found that PBDT-DTN with alkylthienyl side chains possesses stronger pi-pi interactions than PIDT-DTN with alkylphenyl side chains, as the latter's side chains are of higher steric hindrance. In addition, due to the similar constituent moiety to ITIC, PIDT-DTN could exhibit much better miscibility with ITIC than PBDT-DTN. In that case, compared with PIDT-DTN, it is easier for PBDT-DTN to form suitable phase separation with either PC71BM or ITIC, which is beneficial for improving exciton dissociation efficiency, reducing bimolecular recombination, and getting more balanced charge mobilities. Overall, homologous polymers with different chemical structures may demonstrate comparable photovoltaic properties in fullerene-based PSCs but extremely different photovoltaic behaviors in fullerene-free PSCs. This important information provides the guidance for molecular design of polymeric donors to achieve high efficiency in fullerene-free PSCs.