Material design of guest acceptor is always a big challenge for improving the efficiency of ternary organic solar cells (OSCs). Here, a pair of isomeric nonfullerene acceptors based on quinoxaline core, Qx–p-C7H8O and Qx–m-C7H8O, is designed and synthesized. By moving the alkoxy chain attached on side phenyl from meta-position to para-position, both π–π stacking distance and crystallinity are enhanced simultaneously. They obtain the uplifted lowest unoccupied molecular orbital level. Compared to Qx–m-C7H8O, Qx–p-C7H8O exhibits wider absorption spectrum and higher extinction coefficient. Using D18-Cl:N3 as host materials, the addition of guest acceptor Qx–p-C7H8O significantly improves the power conversion efficiency (PCE) from 17.61% to 18.49% because of higher open-circuit voltage (0.875 V) and short-circuit current density (27.85 mA cm−2). This can be attributed to the faster exciton dissociation, more balanced carrier mobility, fine fiber morphology, and lower energy loss in the ternary devices. However, Qx–m-C7H8O-based ternary device achieves relatively low PCE of 17.17% because this device shows extremely low electron mobility. The results indicate that molecular stacking, film morphology, etc., can be effectively modulated by fine-tuning the side chains of guest materials, which may be an effective design rule for further improving the PCE of OSCs.