The implementation of prosecutorial public interest litigation is a profound reform of the judicial system. Its essence is to use judicial power to alleviate the problem of “tragedy of the commons” that may occur due to the absence of subjects in the public interest, which has a far-reaching impact on safeguarding public interests, restraining the dissipation of rent dissipation, and optimizing resource allocation. The existing research results mainly focus on the theoretical basis, institutional value and normative construction of prosecutorial public interest litigation, and there are few empirical analyses on the policy effects of prosecutorial public interest litigation. Based on this, this study takes the pilot data of prosecutorial public interest litigation in China as samples, takes green patent application as the core variable to represent the company’s green innovation, and uses the difference-in-difference model to carry out empirical research, which can comprehensively test the policy effect of prosecutorial public interest litigation system innovation, and reveal the internal mechanism of prosecutorial public interest litigation to promote the company’s green innovation so as to provide empirical evidence for the full implementation of prosecutorial public interest litigation system. It is found that prosecutorial public interest litigation significantly improves the enthusiasm of companies to apply for green patents, and the more transparent the regional prosecutorial organs, the more adequate the supply of environmental testing institutions, and the higher the public attention of companies, the more obvious the policy effect of prosecutorial public interest litigation to promote companies’ green patent applications. Further research shows that the proportion of state-owned shareholding and company size have a positive moderating effect on prosecutorial public interest litigation and corporate green innovation, while the political association of senior executives has a negative moderating effect on both. This research conclusion provides important empirical evidence for clarifying the relationship between prosecutorial public interest litigation and corporate green innovation, helps to further consolidate the social foundation of prosecutorial public interest litigation system innovation, and points out the direction for establishing and improving the supporting system of prosecutorial public interest litigation.