It has been a vital topic for speeding up a high integration of the digital economy and green economic transformation in China's academic and social domains. This paper, based on 2005 to 2020 data of China's 280 cities, uses principal component analysis and non-expected output super-efficiency EBM model to measure cities' digital economic level and green economic efficiency and studies the impacts and mechanism of digital economic development on urban green economic efficiency in consideration of endogeneity and robustness. It concludes that digital economy can effectively improve urban green economic efficiency, and enforce the green economic diffusion effects of middle or large cities over their surrounding cities, which overcomes the echo effect over small cities, helping fulfill network effect which turning “core-periphery” structure by displaying green universal welfare functions on differently sized cities and boosting regional green economy. Improvement of digital economy on green economic efficiency is more where has a higher marketizing level and environmental regulations. Digital economy can promote green innovation and economic agglomeration, driving urban low-carbon growth. This paper presents suggestions for governments on raising support for digital industries, on making differentiated function positioning and strategies for differently sized cities, and on creating a sound marketing and policy environment for an entire green transformation.