Organic semiconductors based upon conjugated frameworks are often isomeric and display distinct optoelectronic properties within minor structural variation. In this work, two isomeric nonfullerene acceptors (NFAs) ThMeCl-1 and ThMeCl-2, having the methyl and chlorine atoms attached on different positions of the electron-withdrawing end group, are synthesized and incorporated as the third component in ternary solar cells. Although these NFA isomers exhibit a similar bandgap, energy levels, and energy loss in their PM6 based binary devices, the efficiency enhancements in ternary devices differ significantly. Compared to ThMeCl-1, the incorporation of ThMeCl-2 in PM6:C5-16 solar cells enables less energy loss, leading to an extra 0.03 eV open-circuit voltage gain and a maximum efficiency increase from 17.8 to 18.9%. Grazing-incidence X-ray diffraction and molecular dynamics simulations reveal that this is attributed to the versatile intermolecular π−π stacking forms between ThMeCl-2 and the host NFA, which result in improved charge transport and suppressed recombination. This work provides a rational guidance for controlling the molecular packing in ternary systems to prepare high performance organic photovoltaics.