Abstract: Based on the three dimensions of input, output and environment about green innovation, this paper innovatively introduces green invention patents and other indicators, and using entropy TOPSIS method and exploratory spatial analysis method, the green innovation capability of 16 prefecture-level cities in Anhui Province in 2018 was comprehensively evaluated and spatial characteristics were analyzed. The results show that the green innovation ability of cities in Anhui Province is generally low, and the comprehensive score of Hefei is much higher than that of other cities in Anhui Province. The spatial distribution characteristics of green innovation capability of prefecture-level cities are obvious, and the cities with higher index are mostly located along the Yangtze River. The green innovation capability of each city shows a certain spatial dependence and spatial correlation.