The organic linkage between the capital market trading system and corporate governance is of great significance in promoting high-quality economic development. Based on the data of A-share listed companies in Shanghai and Shenzhen from 2008 to 2021, this paper examines the governance effect of external supervision of margin trading and short selling on the internal R&D manipulation of enterprises by using the quasi-natural experimental scenarios of China’s margin trading program. It is found that margin trading program, a measure to improve the capital market trading system, has a significant inhibitory effect on the R&D manipulation of enterprises, and the inhibitory effect is more pronounced in non-state-owned enterprises, companies with higher financing constraints, lower quality of internal controls and less analyst attention. The mechanism test shows that the margin trading program has an impact on R&D manipulation through the information transmission effect and the attention gathering effect.