The change in the labor supply structure brought by population aging is not conducive to the improvement of total factor productivity of manufacturing enterprises, but it will prompt enterprises to change their development modes, and promote the improvement of manufacturing enterprises’ total factor productivity through the influence of other factors. Therefore, the relationship between population aging and total factor productivity of manufacturing enterprises is the result of the combined effect of multiple effects, is non-linear, and exhibits heterogeneity. The analysis of A-share listed manufacturing enterprises in Shanghai and Shenzhen from 2000 to 2019 shows that there is an “inverted U-shaped” non-linear relationship between population aging and total factor productivity of manufacturing enterprises. At present, China’s aging population has a significant positive impact on the total factor productivity of manufacturing enterprises, which is most significant in the central region, followed by the eastern region, but not significant in the western region. Population aging will promote the total factor productivity of manufacturing enterprises through increasing labor cost, human capital accumulation and R&D input, etc. It is necessary to optimize and perfect population, education and labor policies, actively explore and create demographic dividend to weaken the negative impact of population aging on labor supply structure, and speed up the transformation of development mode, from relying on the factor-driven demographic dividend to the innovation-driven by the technological dividend, so as to further improve the total factor productivity of enterprises.