Electron transport materials (ETMs) in perovskite solar cells (PSCs) are essential for enhancing photoelectric conversion efficiency, increasing stability, and reducing hysteresis effects. In this work, a series of novel A−DA′D−A type ETMs with an electrondeficient naphthalene diimide (NDI) core as acceptor A′, thiophene rings of different lengths as donors (D), and end groups (A) with different electron-withdrawing ability were designed. The effects of π-conjugation lengths and electronic properties with end-capped engineering, electron transfer mobility, interfacial interaction, and antihumidity have been comprehensively examined using density functional theory (DFT), time-dependent DFT (TD-DFT), and ab initio molecular dynamics (AIMD). The enhanced electron transport and interfacial characteristics along with appropriate energy levels are present in the designed ETMs. Moreover, compared to the parent molecule NDI, the electron mobility of the new ETMs is significantly higher by up to 3 orders of magnitude. In addition, AIMD simulations show that the newly designed molecule NDI-6Th-H has a strong interaction with the perovskite surface, resulting in stronger moisture resistance than NDI. Along with improving knowledge of the structure− property relationship of ETMs, this work offers a set of prospective ETMs for high-performance PSCs.