A series of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM)-like fullerene derivatives with the butyl chain in PCBM changing from 3 to 7 carbon atoms, respectively (F1–F5), are designed and synthesized to investigate the relationship between photovoltaic properties and the molecular structure of fullerene derivative acceptors. F2 with a butyl chain is PCBM itself for comparison. Electrochemical, optical, electron mobility, morphology, and photovoltaic properties of the molecules are characterized, and the effect of the alkyl chain length on their properties is investigated. Although there is little difference in the absorption spectra and LUMO energy levels of F1–F5, an interesting effect of the alkyl chain length on the photovoltaic properties is observed. For the polymer solar cells (PSCs) based on P3HT as donor and F1–F5, respectively, as acceptors, the photovoltaic behavior of the P3HT/F1 and P3HT/F4 systems are similar to or a little better than that of the P3HT/PCBM device with power conversion efficiencies (PCEs) above 3.5%, while the performances of P3HT/F3 and P3HT/F5-based solar cells are poorer, with PCE values below 3.0%. The phenomenon is explained by the effect of the alkyl chain length on the absorption spectra, fluorescence quenching degree, electron mobility, and morphology of the P3HT/F1–F5 (1:1, w/w) blend films.