Ternary solar cells have been rapidly developed in the realm of organic solar cells (OSCs). The incorporation of a third component into a cell results in a complicated active layer morphology, and the relation of this morphology to power conversion efficiency remains elusive. In this work, two ternary active layers, B1:Y7 (10 wt%):BO-4Cl and B1:Y7 (50 wt%):BO-4Cl are constructed, and the reasons for the differences in PCE caused by varying the Y7 content are investigated using theoretical calculations. Firstly, four groups of binary complexes (B1:BO-4Cl-10 wt%, B1:BO-4Cl-50 wt%, B1:Y7-10 wt%, B1:Y7-50 wt%) were examined using molecular dynamics simulation and the stacking patterns of the complexes could mainly be categorized into three groups (IC-T, IC-BDT, IC-RHD). The results showed that with an increase of the Y7 content, the proportion of IC-T stacking decreased while IC-BDT stacking increased. Moreover, the properties of each stacking pattern were calculated and IC-T stacking was found to have a greater charge separation coupling and rate, and a smaller interaction energy. With more IC-T stacking, the number of charge transfer (CT) states and CT mechanisms in B1:BO-4Cl-10 wt% and B1:Y7-10 wt% improves the PCE of B1:Y7 (10 wt%):BO-4Cl. For the trimers, a greater number of CT states and CT pathways can also facilitate efficient charge separation in B1:Y7 (10 wt%):BO-4Cl. Additionally, this work provides basic knowledge of the influence that the third component content on cell performance, providing theoretical instruction for experimental work based on Y-series non-fullerene acceptor materials.