The digital economy centered on digital technology brings high-end digital service elements, empowers the new development of total factor productivity, and becomes the new driving force to promote the high quality of the economy at present. In this context, this paper conducts an empirical research on the relationship between digital economy and enterprise total factor productivity based on the matching data of A-share listed enterprises in Shanghai and Shenzhen and the development of digital economy in cities from 2011 to 2021. The results of the study show that, firstly, the digital economy has a significant contributing effect on enhancing enterprise total factor productivity, and the results still hold after a series of robustness tests. Second, the heterogeneity analysis found that the digital economy has different degrees of influence on enterprise total factor productivity in different regions, especially in the eastern region, this effect is stronger. On this basis, the theoretical content of promoting the construction of digital economy is enriched, and policy recommendations for integrating the development of digital economy and total factor productivity are put forward.