Green innovation (GI) is an important way to build an ecological civilization and an innovative country. The study on urban green innovation (UGI) is of great significance for enriching the research on GI and rationally formulating high-quality urban development policies. The green patent data obtained using a web crawler was used to represent the level of UGI. The spatiotemporal evolution and influencing factors of UGI in China were analyzed by standard deviation ellipses, spatial autocorrelation, and Geodetector. The research shows that: From 2005 to 2020, the level of UGI in China tended to rise rapidly. The center of gravity of UGI in China was located in the southeast of China's geometric center and tended to move to the south and west. The standard deviation ellipse was distributed in a “northeast-southwest” pattern, the area was gradually shrinking, and the length of the two semi-axes was shortening. UGI in China showed obvious global and local spatial autocorrelations. The degree of global spatial autocorrelation was gradually increasing. Among the types of local spatial autocorrelation, the largest number of low-low agglomeration cities was mainly located in the northwest and southwest part of China, while high-high agglomeration cities were distributed in Beijing-Tianjin-Hebei, Yangtze River Delta, and Pearl River Delta. The government intervention expressed by the proportion of scientific and technological expenditure in fiscal expenditure and environmental regulation is the dominant factor affecting UGI.