An evaluation system of digital economy and green technology innovation was constructed based on 271 cities at prefecture-level and above in China. The coupling coordination degree model was used to measure the coupling coordination degree of digital economy and green technology innovation, and the regional differences and spatial effects were analyzed. The results show that the coupling coordination degree of urban digital economy and green technology innovation in China shows an upward trend from 2013 to 2018, but the absolute value of coupling coordination degree is only in the moderate coupling type, and the coupling coordination degree shows significant regional and urban differences. The Dagum Gini coefficient shows that the regional differences of coupling coordination degree between digital economy and green technology innovation show a downward trend during the observation period. The regional differences of coupling coordination degree of seven regions mainly come from the super-variable density, and the regional differences of coupling coordination degree of different types of cities mainly come from the inter-group differences. Moran index shows that the coupling coordination degree of digital economy and green technology innovation has significant spatial effect, and this spatial effect has significant regional differences. Finally, corresponding policy suggestions are put forward based on the research conclusions of this paper.