Developing a design strategy to establish the compatibility of acceptor materials with donor materials is important for the rational development of organic solar cells. We synthesized 2,6-dimethoxyphenyl methanofullerene derivatives to realize an enhanced open-circuit voltage, and we investigated polarities and their effects on the film morphology of the active layer. The polarities of the synthesized fullerene derivatives were affected significantly by the presence of functional groups, such as methoxy, ether, and ester groups. Macro/nanoscopic morphological investigation and spectroscopic analysis of the blend films of the poly(3-hexylthiophene)(P3HT)/fullerene derivatives showed that a balanced polarity between materials results in the formation of optimized nanomorphology without grains and robust phase separation. Measurements of the device performance of the photovoltaic cells composed of P3HT and the fullerene derivatives confirmed the same tendency as that shown in the morphological analysis. This finding enables us to obtain an improved power conversion efficiency because of the enhanced open circuit voltage derived from the fullerene derivatives.