For bulk heterojunction organic solar cells (OSCs), controlling molecular self‐aggregation during solution processing is crucial to obtain ideally phase‐separated morphology and high device performance. Recently, fused‐ring regiochemistry, for example, carbon–oxygen (CO)‐bridge isomerization, has been found to effectively modulate the aggregation structures and photovoltaic properties of acceptor–donor–acceptor (A–D–A) small‐molecule acceptors (SMAs). Strikingly, the relative aggregation ability for the CO‐bridge isomers turns out to be reverse after simultaneous replacement of the linear alkyl side chains with branched ones and fluorination of the end groups. Herein, to understand the molecular origin of such an observation, the aggregation behaviors of three pairs of CO‐bridge isomeric SMAs in solutions are systematically investigated by atomistic molecular dynamics simulations. Because of the large side‐chain steric hindrance around the fused‐ring core, the molecular self‐aggregation for all of these SMAs is dominated by end‐group π–π stacking. Moreover, the end‐group π–π interaction is controlled by the synergistic effect of CO‐bridge isomerization, side‐chain branching, and end‐group fluorination, which are responsible for the reversal of the aggregation ability of the isomeric SMAs. This work provides the rationalization of experimental observations and is helpful for modulating the blending morphologies for high‐efficiency OSCs based on CO‐bridge SMAs.