The development of high-performance organic solar cells (OSCs) with high operational stability is essential to accelerate their commercialization. Unfortunately, there is currently a lack of detailed understanding of the origin of instabilities in state-of-the-art OSCs based on bulk heterojunction (BHJ) featuring non-fullerene acceptors (NFAs). Herein, we developed NFA-based OSCs using different charge extraction interlayer materials and studied their storage, thermal, and operational stabilities. Despite the high power conversion efficiency (PCE) of the OSCs (17.54%), we found that cells featuring self-assembled monolayers (SAMs) as hole-extraction interlayers exhibited poor stability. The time required for these OSCs to reach 80% of their initial performance (T80) was only 6 h under continuous thermal stress at 85 °C in a nitrogen atmosphere and 1 h under maximum power point tracking (MPPT) in a vacuum. Inserting MoOx between ITO and SAM enhanced the T80 to 50 h and ~15 h after the thermal and operational stability tests, respectively, while maintaining a PCE of 16.9%. Replacing the organic PDINN electron transport layer with ZnO NPs further enhances the cells’ thermal and operational stability, boosting the T80 to 1000 and 170 h, respectively. Our work reveals the synergistic role of charge interlayers and device architecture in developing efficient and stable OSCs.