The development of hole-transporting materials (HTMs) that can passivate defects in perovskite is of great significance in improving the efficiency and long-term stability of perovskite solar cells. To date, the investigation on HTMs mainly focus on exploring new structures, while molecular configuration is seldomly concerned. In this work, two small molecules are developed as HTMs with benzil and phenanthrene quinone as the core structure, respectively. With similar structure and the same defect passivation groups, whereas, the two molecules exhibit different configurations, thus distinct properties. Compared to 3,6-bis(3,6-bis(bis(4-methoxyphenyl)amino)-9H-carbazol-9-yl)phenanthrene-9,10-dione (PQ) with a rigid core structure, the benzil group in 1,2-bis(4-(3,6-bis(bis(4-methoxyphenyl)amino)-9H-carbazol-9-yl)phenyl)ethane-1,2-dione (DB) is flexible and can adjust molecular configuration to efficiently interact with the underlying perovskite material, which is confirmed from both experimental results and theoretical simulations. The DB-based device exhibits a high power conversion efficiency of 22.21% with excellent long-term stability, superior to the PQ-based device (20.22%). This work demonstrates that molecular configuration engineering will directly affect the properties of hole transport materials, as well as their interactions with perovskite, which should also be taken into consideration when devising HTMs.