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A low band-gap polymer, PTB7-Th, is one of the typical p-type semiconductors among the next-generation solar-cell materials that have achieved power conversion efficiencies of over 10%. However, the internal deterioration mechanism of high-efficiency polymer solar cells such as PTB7-Th-based cells is still an open issue and has been extensively studied. Here, we report a study with operando electron spin resonance (ESR) spectroscopy for PTB7-Th polymer solar cells with an n-type semiconductor PC 71 BM to clarify the internal deterioration mechanism at a molecular level. We have directly observed ambipolar charge accumulation with a face-on molecular orientation in the cells under simulated solar irradiation using an operando light-induced ESR technique. Moreover, we have found a clear correlation between the charge accumulation and performance deterioration of the cells. The charge accumulation sites have been clarified by the ESR analysis and density functional theory calculation. The prevention of such charge accumulation on the basis of the present finding would be important for the commercialization of high-efficiency polymer solar cells.