This paper investigates the impact mechanism of digital economy on total factor productivity, based on a quasi-natural experiment in the national-level big data comprehensive pilot zone, using panel data of 280 prefecture-level cities from 2014 to 2019, and empirical tests using the multi-period double-difference method. The results show that: the digital economy significantly enhances total factor productivity, and this conclusion still holds after multiple robustness tests; the mediation effect test shows that the digital economy enhances total factor productivity by improving the efficiency of resource allocation and promoting technological innovation; the heterogeneity analysis shows that the digital economy has a promotional effect and suppresses the total factor productivity of cities with high resource endowment and high digital economy, while the effect on non-smart cities is not obvious. Therefore, the direct and indirect role of the digital economy should be deeply explored based on the comprehensive pilot zone of big data, and differentiated development strategies should be adopted to cultivate and strengthen new drivers of total factor productivity growth.