Fluorine side chain functionalization of non‐fullerene acceptors (NFAs) represents an effective strategy for enhancing the performance of organic solar cells (OSCs). However, a knowledge gap persists regarding the relationship between structural changes induced by fluorine functionalization and the resultant impact on device performance. In this work, varying amounts of fluorine atoms were introduced into the outer side chains of Y‐series NFAs to construct two acceptors named BTP‐F0 and BTP‐F5. Theoretical and experimental investigations reveal that side‐chain fluorination significantly increase the overall average electrostatic potential (ESP) and charge balance factor, thereby effectively improving the ESP‐induced intermolecular electrostatic interaction, and thus precisely tuning the molecular packing and bulk‐heterojunction morphology. Therefore, the BTP‐F5‐based OSC exhibited enhanced crystallinity, domain purity, reduced domain spacing, and optimized phase distribution in the vertical direction, facilitating exciton diffusion, suppresses charge recombination, and improves charge extraction. Consequently, the promising power conversion efficiency (PCE) of 17.3% and 19.2% were achieved in BTP‐F5‐based binary and ternary devices, respectively, surpassing the PCE of 16.1% for BTP‐F0‐based OSCs. This work establishes a structure‐performance relationship and demonstrates that fluorine functionalization of the outer side chains of Y‐series NFAs is a compelling strategy for achieving ideal phase separation for highly efficient OSCs.