Green innovation is significant in realizing enterprises’ green transformation and high-quality economic development. Using the data of China’s Shanghai and Shenzhen A-share listed companies from 2009 to 2019, this study divides enterprise green innovation into substantive and strategic innovations and analyzes the impact of government subsidies on green innovation and the mediating role of R&D investment. The research results show that: (1) Government subsidies promote enterprises’ substantive and strategic green innovation, with the impact on substantive innovation being more significant. (2) Government subsidies can help stimulate enterprises to increase R&D investment, promoting green innovation. R&D investment is an important intermediary between government subsidies and enterprise green innovation. (3) R&D investment has a more significant mediating effect on the green innovation of state-owned enterprises, large enterprises, non-polluting industries, and enterprises in non-carbon emission trading pilot areas. Therefore, the government should formulate differentiated subsidy policies according to enterprises’ internal and external conditions and improve the carbon emission trading system. In contrast, enterprises should actively adapt to policy changes and rationally use policy resources.