Based on the practical requirements of deepening the implementation of the innovation driven development strategy and accelerating the construction of a strong country in science and technology, the level of innovation investment in various regions of China continues to increase, but there are still regional differences. Using panel data from 30 provinces, regions, and cities in China from 2011 to 2019, a spatial econometric model is constructed to test the impact of national audit on regional innovation investment. The research results indicate that national auditing can significantly improve the level of regional innovation investment, and this impact has a dual lag in space and time. That is, national auditing not only promotes the improvement of local innovation investment levels, but also has spatial spillover effects between different provinces, and this impact will continue until the next year. Further research has found that compared to the functions of resistance and prevention, the disclosure function of national auditing can significantly enhance regional innovation investment. The role of national auditing in enhancing innovation investment is more significant in the central and eastern regions. There is also a spatial spillover effect of national audits on regional innovation output. The relevant conclusions remain robust even after replacing the measurement indicators of the explanatory variable and the dependent variable. The research findings have important implications for fully leveraging the national audit supervision function and promoting regional innovation and coordinated development.