The degradation mechanism of pentacene/fullerene (C60)-based photovoltaic device is studied as a function of heating time. The efficiency of the device with bathocuproine (BCP) as buffer layer shows a considerable decay from 1.49 to 0.6% after 168-h heating, whereas the device without BCP possessed a stable performance under heating treatment. This decay is mainly caused by the poor thermal stability of BCP, which crystallized after the heating treatment and is discussed through the incident photon-to-electron conversion efficiency (IPCE) and the atomic force microscopic (AFM) measurements. The IPCE results indicated the redistribution of optical field due to the crystallization of BCP, and the AFM images showed the significant increase in surface root-mean-square value from 0.46 to 24.7 nm. Furthermore, the device without BCP exhibited the decrease in series resistance (Rs). The reduced Rs was attributed to the polycrystallized-like molecular arrangement after heating, which was confirmed by the Gaussian-disordered model.