Abstract: Exploring the impact mechanism of rural population aging on agricultural total factor productivity has a certain practical enlightenment for accelerating agricultural modernization and positive effect for coping with population aging in China. Based on China’s provincial panel data from 2004 to 2019, this paper calculates the agricultural total factor productivity of 30 provinces and cities in China with the help of Malmquist index method. Through the intermediary effect model, this paper explores the impact mechanism of rural population aging on agricultural total factor productivity from five aspects: labor supply quantity effect, labor supply quality effect, technology experience accumulation effect, technology renewal effect and capital investment effect. Finally, taking the northeast and southwest regions as examples, the regional differences of this mechanism are further analyzed. It can be found that at this stage, the inhibition effect of rural population aging on agricultural total factor productivity is stronger than the promotion effect. From the national level, the aging of rural population inhibits the agricultural total factor productivity through the quantity, quality and capital investment of labor supply, and promotes the agricultural total factor productivity through the accumulation of technological experience and technological renewal. However, according to the results of subregional research, this test result is not completely consistent with that of northeast and southwest regions. Therefore, when formulating corresponding policies, we should adjust measures to local conditions and comprehensively consider the differences between various regions.