Central π-core engineering of non-fullerene small molecule acceptors (NF-SMAs) is effective in boosting the performance of organic solar cells (OSCs). Especially, selenium (Se) functionalization of NF-SMAs is considered a promising strategy but the structure-performance relationship remain unclear. Here, we synthesize two isomeric alkylphenyl-substituted selenopheno[3,2-b]thiophene-based NF-SMAs named mPh4F-TS and mPh4F-ST with different substitution positions, and contrast them with the thieno[3,2-b]thiophene-based analogue, mPh4F-TT. When placing Se atoms at the outer positions of the π-core, mPh4F-TS shows the most red-shifted absorption and compact molecular stacking. The PM6:mPh4F-TS devices exhibit excellent absorption, high charge carrier mobility, and reduced energy loss. Consequently, PM6:mPh4F-TS achieves more balanced photovoltaic parameters and yields an efficiency of 18.05%, which highlights that precisely manipulating Se is a practicable way toward high-efficiency OSCs.