This paper constructs the measurement index system of digital economy, reasonably measures the input and output of digital economy, estimates the efficiency of China's digital economy through DEA model, and then explores the factors affecting the efficiency of digital economy through Tobit regression model. The results show that the efficiency of China's digital economy generally does not reach DEA effectiveness, and shows a trend of rising first and then falling. Some factors will have a positive effect on the efficiency of digital economy. In addition, when the economic resources invested do not match the development needs of digital economy, they have a negative effect on the efficiency of digital economy. It is urgent for all regions to optimize the allocation of resources and promote the efficient development of digital economy.