Fullerene derivatives are considered excellent materials for the extraction and transportation of electrons in the production of efficient tin-based perovskite solar cells (TPSCs). However, it is not clear how the molecular structure of fullerene derivatives affects the efficiency and stability of TPSCs. In this study, the effects of fullerene derivatives, (6,6)-phenyl-C61-butyric acid hexyl ester (PCBH) and (6,6)-phenyl-C61-butyric acid methyl ester (PCBM), with different functional groups, on photovoltaic performance were investigated. The flexible alkyl chain of PCBH effectively improved the film morphology and stability, the electron extraction and transport capabilities, and the interface contact of fullerene and perovskite. As a result, the PCBH-based TPSC yielded a higher efficiency, of 9.21%, than the PCBM-based devices (7.54%). More importantly, the PCBH-based films exhibited higher stability and effectively suppressed the oxidation of Sn2+ by inhibiting oxygen permeation. Therefore, the PCBH-based devices exhibited significantly enhanced stability. This result indicates that optimizing the functional group of fullerene derivatives is crucial for improving the efficiency and stability of TPSCs.