Based on 2003—2018 China Provincial panel data, the index disclosed in the Evaluation Report of China's Regional Innovation Capability is used to measure regional innovation capability, and the influence of the supervision mechanism from government audit on regional innovation capability is empirically tested. It is found that the governance functions of government audit, such as information transmission, behavior deterrence and system correction, enhance regional innovation capability. Further exploration of function path shows that government audit improves regional innovation ability by improving government governance efficiency and resource allocation efficiency. Heterogeneity analysis shows that the incentive effect of government audit on regional innovation capability is more obvious in the regions with less promotion pressure and stronger institutional environment.