Bilayer organic solar cells (OSCs) have been actively investigated due to more ideal photoactive layer structures and possibly better device stability compared to those of bulk-heterojunction OSCs. Here, we introduce a binary non-fullerene acceptor layer composed of IDIC and IT-4F into bilayer OSCs and investigate its effects on device performance and thermal stability. We found that IT-4F suppresses IDIC aggregation, which provides ideal interface morphologies between acceptor and electron transport layers, resulting in improved power conversion efficiency. In addition, due to suppressed IDIC aggregation, PM6/IDIC:IT-4F films showed robust thermal durability upon various pre-annealing test conditions. Moreover, PM6/IDIC:IT-4F bilayer OSCs exhibited improved stability compared to that of PM6/IDIC devices under continuous thermal annealing conditions. Whereas all photovoltaic parameters deteriorated upon thermal annealing in PM6/IDIC devices, only open-circuit voltages were reduced in PM6/IDIC:IT-4F devices, possibly due to a minor aggregation of IDIC. Nevertheless, binary acceptor layer reduced non-radiative voltage losses in bilayer OSCs, suggesting that there is more room to achieve better device stability by proper material selection. This work demonstrates that introducing a binary acceptor layer into bilayer OSCs can be an effective strategy to achieve both high efficiency and improved stability, especially when the given NFA tends to aggregate strongly.