Y‐series non‐fullerene acceptors (NFAs) have achieved great progress in organic solar cells (OSCs). Most research attention is currently paid to their molecular engineering to improve the efficiency of OSCs. However, as n‐type organic semiconductors, the relationship between their molecular packing structures and charge transport properties is mostly ignored. Herein, it is clarified how the molecular packing of Y‐series NFAs fundamentally determines their charge transport properties by manipulating their crystal stacking via sidechain engineering. Therefore, branched alkyl/alkoxy substitutions are taken on a reference NFA (Y6‐1O), affording three derivatives, namely 1OBO‐1, 1OBO‐2, and 1OBO‐3. Results show that while the replacement of branched alkyl/alkoxy sidechains has little impact on optical properties and energy levels, it can change crystal stacking motifs significantly. The single crystal of Y6‐1O with all linear sidechains forms a 2D‐brickwork structure and shows lower mobility. In contrast, 1OBO‐2 with all branched sidechains exhibits a favorable 3D interpenetrating porous network, displaying an electron mobility of 1.42 cm2 V−1 s−1 in single‐crystal organic field‐effect transistors (SC‐OFETs). This value is among the highest for NFA‐based n‐type OFETs. This study not only reveals the fundamental structure–property relationships of Y‐series NFAs, but also suggests the potential of Y‐series NFAs for high‐performance n‐type organic semiconductors.