Abstract Fullerene derivatives are widely employed as efficient electron-transporting layers (ETLs) in p-i-n perovskite photovoltaics but face challenges in mitigating interfacial recombination losses and ensuring stable film morphology. Non-fullerene acceptors (NFAs), commonly utilized in organic photovoltaics, present a promising alternative to fullerene-based ETLs. Nevertheless, the suboptimal performance of NFA-based devices underscores the need for molecular engineering to tailor their properties. Herein, we develop two Y-type NFAs, Y-Phen and Y-CE, by substituting the benzothiadiazole core of Y6 with higher-polarity phenanthroline and crown ether. These modifications effectively enhance carrier kinetics by (1) promoting ordered molecular assembly on the perovskite surface through supramolecular interactions, thereby optimizing interfacial energetic alignment, and (2) improving the molecular packing to facilitate efficient charge transport. Using Y-CE as the ETL, the device achieves a certified power conversion efficiency (PCE) of 25.59%. Furthermore, the optimized device exhibits less than 10% degradation in PCE after 1440 hours of thermal aging. This work offers valuable insights into designing NFA-based ETLs for high-performance perovskite photovoltaics.