Side-chain engineering has been demonstrated as an effective method for fine-tuning the optical, electrical, and morphological properties of organic semiconductors toward efficient organic solar cells (OSCs). In this work, three isomeric non-fullerene small molecule acceptors (SMAs), named BTP-4F-T2C8, BTP-4F-T2EH and BTP-4F-T3EH, with linear and branched alkyl chains substituted on the α or β positions of thiophene as the side chains, were synthesized and systematically investigated. The results demonstrate that the size and substitution position of alkyl side chains can greatly affect the electronic properties, molecular packing as well as crystallinity of the SMAs. After blending with donor polymer D18-Cl, the prominent device performance of 18.25% was achieved by the BTP-4F-T3EH-based solar cells, which is higher than those of the BTP-4F-T2EH-based (17.41%) and BTP-4F-T2C8-based (15.92%) ones. The enhanced performance of the BTP-4F-T3EH-based devices is attributed to its stronger crystallinity, higher electron mobility, suppressed biomolecular recombination, and the appropriate intermolecular interaction with the donor polymer. This work reveals that the side chain isomerization strategy can be a practical way in tuning the molecular packing and blend morphology for improving the performance of organic solar cells.