The panel data of 50 new energy vehicle enterprises in Shanghai and Shenzhen A-shares from 2012 to 2021 are selected to empirically analyze the impact of government subsidies on the innovation of new energy vehicle enterprises and to further discuss the differences between such an impact in different forms and regions. The study finds that, first, government subsidies have a certain promotion effect on the innovation of new energy vehicle enterprises, and an inverted U-shaped relationship exists thereof. Second, at the enterprise level, government subsidies have a significant effect on the innovation of non-state enterprises, downstream vehicle enterprises, and enterprises with lower establishment years, and the inverted-U trend is evident. Third, at the regional level, government subsidies have a more significant effect on the innovation of enterprises in non-eastern regions and low-environmental regulation regions, and the inverted-U-shaped relationship trend is more apparent. The study establishes the nonlinear relationship between government subsidies and the innovation of new energy vehicle enterprises through empirical research, which expands the theory of enterprise innovation and has a certain guiding significance for improving the innovation capability of new energy vehicle enterprises in the future.