It is of great reference value to study the evolution trend and the source of differences of regional digital economy development for the realization of coordinated and high-quality development in China. Based on the panel data of 30 provinces, regions and cities from 2012 to 2020, entropy method is used to measure the development level of digital economy in the whole country and eight comprehensive economic zones, and Markov chain and Kernel density estimation are used to explore the spatial-temporal evolution characteristics of digital economy development. Dagum Gini coefficient and variance decomposition model are used to reveal the spatial and structural sources of development differences in digital economy. The research shows that the development level of digital economy in China as a whole and in all regions is increasing year by year, but the eight comprehensive economic zones show an unbalanced pattern of decreasing gradient of “eastern coastal area -southern coastal area -northern coastal area -middle reaches of Yangtze River -middle reaches of Yellow River -Northeast -Northwest area”. The spatial and temporal evolution characteristics show that the development of provincial digital economy is usually accompanied by spatial effect and “agglomeration” effect, and there is a certain probability of internal mobility. At the same time, the evolution trend and polarization characteristics of kernel density curve indicate that there is regional heterogeneity in the development of digital economy. The spatial difference decomposition shows that the overall difference of digital economy development shows a trend of fluctuation and decline, and the regional difference is the main source. The decomposition of structural difference shows that the development gap of digital industrialization, industry digitization and digital infrastructure is the main structural source of the development difference of digital economy. This study can help improve the spatial pattern of digital economy development and create new advantages of regional digital economy industry. Therefore, it is suggested that the government should break down regional barriers and further strengthen infrastructure construction while promoting the deep integration of digital industry.