Due to the development of efficient non-fullerene acceptors with excellent crystallinity and effective inter-mixing with donor polymers, the power conversion efficiencies (PCEs) of organic solar cells (OSCs) have reached levels suitable for commercial implementation. Nonetheless, the poor operational stability of these OSCs remains a significant bottleneck, limiting their practical application and necessitating immediate attention. In an effort to address this issue, in the present study, we investigate the active layers fabricated using four different acceptors (BTP4F, IT4CL, IT4F, and PC71BM) blended with a conjugated polymer donor (PBDBT-2F). The corresponding OSCs demonstrate distinctly different π-π stacking characteristics. We utilize operando experiments to examine the temporal evolution of the active layer morphology as the OSCs operate under AM 1.5 G light illumination. We discover that, after device operation, the active layer for all types of devices develops a finer structure with more isolated domains, particularly for larger-sized domains. In addition, the morphology of the middle-sized domains is more influenced at the initial operating stage of OSCs with relatively poor π-π stacking, resulting in a more severe performance decay of these devices. Moreover, the decrease in PCE is primarily attributed to a decrease in the fill factor (FF), with decay curves displaying a similar trend to the structural shrinkage. Notably, we observe that the stability of the active layer morphology in the device geometry is not optimal for well-intermixed donor-acceptor systems with notable face-on crystallinity compared to slightly de-mixed donor-acceptor systems with good π-π stacking. This behavior is consistent with the different degrees of resilience of device performance.