Poor operation stability is a major hurdle for the wide application of organic photovoltaic (OPV) devices. While most attention is given to environmental threats to device stability, we herein show evidence from X-ray photoemission spectroscopy (XPS) of an intrinsic time-dependent chemical reaction at a donor/acceptor interface. Albeit with impressive device performance from boron subphthalocyanine chloride (SubPc)/fullerene (C60) interface, the forming boride bonds at its interface hinders the interfacial exciton dissociation and leads to device deterioration. Due to the high electron affinity of molybdenum oxide (MoO3) film, the incorporation of MoO3 layer under the SubPc film has strong electron-drawing property and leads to charge-transfer complex (CTC) formation at the MoO3/SubPc interface. The resulting charge redistribution in SubPc molecules effectively suppresses the further interfacial reaction at SubPc/C60 junction. Our results provide insight for new degradation mechanisms of OPV devices and corresponding stability control via charge redistribution in the donor film.