Non-fullerene acceptors (NFAs) have boomed in the field of organic solar cells (OSCs); however, the charge generation mechanism remains elusive owing to the complex molecular stacking patterns in the active layer and numerous selections of the donor and acceptor for practical OSCs. Herein, we built 178 interfacial models consisting of molecules M-Phs and BTP-eC9 as the donor (D) and acceptor (A), respectively, to reveal the relationship between the molecular stacking patterns and charge-transfer (CT) mechanisms. After obtaining the optimized D/A structures, we divided the 178 D/A dimers into different groups (T-S, C-S, N-N groups) based on the molecular stacking pattern by positional parameters (i.e., centroid distance and angle) and calculated their interfacial properties. The results indicate that multichannel exciton dissociation mechanisms exist in the M-Phs/BTP-eC9 active layer (i.e., hot exciton and direct excitation mechanisms, the intermolecular electric field (IEF) mechanism, and hole transfer) and the different CT mechanisms are mainly attributed to changes in the stacking patterns caused by the different portions of the acceptor approaching the skeleton of the donor. We further classified the group with the terminal unit of the acceptor inclined to approach different portions of the donor skeleton in detail by a molecular orientation (face-on, edge-on, and slipped), and we found a strong correlation between the energy of the lowest charge-transfer state (ECT) and the distance of the centroid between the terminal unit of the acceptor and the π bridge of the donor. This work provides a robust description of the relationship between molecular stackings and CT mechanisms, suggesting the crucial role of D and A arrangements in the NFA-based active layer.