The active layer morphology of non-fullerene organic solar cells is one of the key factors affecting the power conversion efficiency (PCE); however, current experimental techniques cannot be used to directly observe the structural information at the electronic level. Molecular dynamics simulations and quantum chemical calculations provide effective means to explore the morphology and properties of active layers. In this paper, the local molecular stacking of PM6:Y6 films is simulated based on ab initio molecular dynamics (AIMD), and the simulation results show that the donor–acceptor (D–A) molecules are pi–pi stacked and some Y6 molecules are arranged in order. The excited state information of PM6:Y6 dimers was calculated by time-dependent density functional theory (TD-DFT) calculations. The results showed that ΔE_S1–CT < 0.1 eV, and dimers have very low exciton binding energy (E_b). The charge transfer processes of the D–A dimer are LE → CT_X → CS and LE → CT_X → CT₁ → CS combined with hole–electron analysis. Moreover, ultraviolet-visible (UV-vis) spectra of J-type stacked dimers is similar to that of PM6:Y6 films. Finally, the electron transfer rates (k_electron) and hole transfer rates (k_hole) were calculated by Marcus theory, and the results showed that the PM6:Y6 system has high charge transfer rates, but the effect of molecular configuration on k_electron is less than that on k_hole. The properties of PM6:Y6 films were systematically investigated at the theoretical level in this work, and it demonstrated that PM6:Y6 films have pi–pi stacking, low ΔE_S1–CTX, low E_b, and high charge transfer rates.