The transformation of China’s economic development mode depends on the high-quality development of the digital economy industry, and the proposal of the concept of green development provides a new direction for promoting the digital economy to promote the upgrading of China’s industrial structure. Based on the data of 290 prefecture-level cities in China from 2011 to 2018, this paper analyzes the impact of digital economy development on green total factor productivity (GTFP) through the fixed effect model. The results show that the development of the digital economy significantly promotes GTFP, and the results are still valid after a series of robustness tests. The development of the digital economy has heterogeneous effects on GTFP, especially in the central and western regions, regions with a low productivity index, and regions with a low industrial structure level. This study provides a useful reference for cities to use the digital economy to promote the development of green economies.