This paper selects A-share listed companies in Shanghai and Shenzhen of China from 2010 to 2019 as research samples, and empirically tests the relationship between environmental protection investment, government intervention and breakthrough innovation of enterprises. The research shows that enterprises' investment in environmental protection can significantly promote the level of breakthrough innovation, and the government's intervention can regulate the relationship between them. Firstly, it is found that government subsidies can strengthen the promotion of environmental protection investment to the level of breakthrough innovation. Furthermore, it explores the regulating effect of market monopoly intensity on the relationship between them, and finds that in industries with high degree of monopoly, the promoting effect of environmental protection investment on the level of enterprise breakthrough innovation will be transformed into inhibiting effect, which shows the importance of government anti-monopoly measures between environmental protection investment and enterprise breakthrough innovation.