The objective of this paper is to measure the efficiency loss of green innovation caused by local government competition and explore its causes and evolution characteristics. Based on the equimarginal principles such as the deviation of the allocation of green innovation output factors, this paper uses the panel data of China’s provinces (excluding Tibet, Hong Kong, Macao and Taiwan) from 2000 to 2020 and employs the spatial panel measurement model and the Kernel density estimation. The study finds that first, local government competition causes the mismatch of local innovation factors not only locally but also in neighboring regions. Second, the mismatch of innovative talents and capital caused by local government competition lowers the green innovation efficiency. Third, the shortage of innovative talents caused by local government competition is the main reason for the loss of green innovation efficiency in Beijing, Tianjin, and Shanghai. Fourth, the degree of efficiency loss of green innovation at the provincial level in China is heterogeneous in government competition strategies, and the loss due to tax competition is the most significant. Fifth, although the loss of green innovation efficiency generally decreases yearly, in the future, the institutional competition will still hinder the improvement of green innovation efficiency in the eastern, central and western regions of China. Our policy suggestions include promoting regional cooperation and cultivating innovative talents to further improve the efficiency of green innovation.