A novel non-volatile additive, fluorinated bis(perfluorophenyl)pimelate (BF7), is demonstrated to effectively improve both the efficiency and thermal stability of a highly efficient organic solar cell (OSC), comprising fluorinated Y6 as the small-molecule acceptor and PM6 as the polymer donor. Processed with optimized 0.5 wt% BF7 in solution, the PM6:Y6:BF7 device achieves an elevated power conversion efficiency (PCE) of 17.01%, compared to 15.16% of that processed without BF7. Moreover, the BF7-elevated PCE can sustain 95% of the best PCE over 100 °C annealing for 72 h. Grazing incidence X-ray scattering and differential scanning calorimetry results consistently indicate that BF7 in the PM6:Y6:BF7 device interacts preferentially with Y6, resulting in improved fractal-like network structures of the active layer with optimized size and orientation of Y6 nano-crystallites and elevated thermal stability. Molecular simulation also supports that the observed structure and thermal stability is associated with the F–π noncovalent supramolecular interactions between the perfluorophenyl moieties of BF7 and difluorophenyl-based FIC-end-groups of Y6. Similar bifunctional BF7 effects are also observed in the well-known PM6:IT-4F system, suggesting that adding BF7 for concomitantly improved PCE and thermal stability might extend generally to OSCs that feature small molecule acceptors of difluorophenyl end-groups.