Based on the quasi-natural experiment of the Ministry of Finance's special inspection of the accounting information of pharmaceutical companies, the effect of government financial supervision on the research and development (R&D) manipulation of pharmaceutical companies was examined. It is found that government financial supervision can effectively curb the R&D manipulation of pharmaceutical companies. This governance effect mainly comes from two mechanisms of "internal and external improvement". First, as a supplementary mechanism of internal governance in pharmaceutical companies, it exerts a governance effect on R&D manipulation. It is found that when the internal control of pharmaceutical companies is weaker and the governance ability of independent directors is poorer, the governance effect of government financial supervision on R&D manipulation is more significant. Second, as a collaborative mechanism of external supervision, it exerts a collaborative governance effect on R&D manipulation. It is found that when external supervision such as media supervision or tax authority supervision is stronger, the governance effect of government financial supervision on R&D manipulation is more significant. Further research shows that the special financial supervision of pharmaceutical companies by the government also has an industry-wide warning effect. It is found that compared with other industries that have not been subject to financial supervision, the degree of R&D manipulation in the pharmaceutical industry that has been subject to government financial supervision is lower. Therefore, when conducting financial supervision, government financial departments should adopt targeted supervisory measures based on the internal governance status of companies and the strength of external supervision.