Taking the provincial panel data from 2006 to 2019 as samples, using the mediation effect test step by step and Sobel test, and taking the government innovation preference as the intermediary variable, this paper discusses the influence of national audit on regional innovation capability. The findings are as follows: national audit can improve regional innovation ability, and local government innovation preference plays a partial intermediary role. Further divided by eastern, central and western regions, the above effects differ significantly, among which, the central regions have the most significant effect of national audit disclosure, which can improve government innovation preference and thus regional innovation ability; national audit suggestions in the eastern regions have the best effect and can promote regional innovation ability through enhancing innovation preference.