The digital economy has aroused widespread concern. This paper studies the impact of the digital economy on innovation using a panel threshold model. Taking 30 provinces, municipalities, and autonomous regions in China as the research object, the time span is from 2013 to 2019. The data are from the National Bureau of Statistics of China (NBSC), China National Intellectual Property Administration (CAIPA), the China Stock Market and Accounting Research (CSMAR), and the Ministry of Industry and Information Technology (MIIT)of China. Data analysis is performed with ArcGIS 10.2 and STATA 16 software. The influence mechanism of digital economy on innovation is innovatively analyzed from the aspects of innovation elements, innovation tools, innovation subjects, and innovation environment. A digital economy development level index system is constructed using the entropy method, and the development level of China’s digital economy in time and space is analyzed. On this basis, the nonlinear impact of digital economy on innovation, i.e., the threshold effect, is innovatively studied using the panel threshold model. It is found that China’s digital economy develops rapidly, but there is a serious spatial imbalance, and there are great differences in the different dimensions of the digital economy. At the same time, the impact of digital economy on innovation has a double threshold effect with industrial structure as the threshold variable and a single threshold effect with urbanization level as the threshold variable. Specifically, the promoting effect of digital economy on innovation increases with the optimization of industrial structure or the improvement of urbanization level. This study enriches the theoretical research on the impact of digital economy on innovation, and it has important support and reference value for China’s development of digital economy and improvement of innovation capacity.