The field of organic solar cells (OSCs) has acquired rapid progress with the development of nonfullerene acceptors. Interfacial engineering is also significant for the enhancement of the power conversion efficiency (PCE) in OSCs. Among the cathode interfacial materials (CIMs), perylene diimide (PDI) small molecules are promising owing to the excellent electron affinity and electron mobility. Although the well-known PDINN molecule has excellent properties, it has a high planarity formed by an extensive rigid π-conjugated backbone. Because the PDI molecular backbone has a strong tendency to aggregate, it causes the problem of excessive molecular aggregation and stacking, which directly leads to excessive crystallinity. Proper accumulation is beneficial for charge transport, but oversized crystals formed by overaggregation will hinder charge transport, ultimately affecting the film morphology and charge transport efficiency. Modifying the bay position of PDINN is an effective strategy to reduce the planarity, modulate the molecular aggregation, optimize the morphology, and enhance the charge-collecting efficiency. Therefore, PDINN-S was synthesized from PDINN by substituting the hydrogen with thiophene. The optimal PCE in the PM6:Y6 active layer was 16.18% and remained at 80% of the initial value after 720 h in a glovebox. This provides some guidance for exploring CIMs and preparing large-scale OSCs in the future.