The informatization development of national audit contributes to the construction of national governance supervision system. It not only systematically corrects deviations ex-post but also enhances the preventive mechanism effectiveness of national audit through dynamic audit, fundamentally improving the formulation and implementation of local government policies and thereby boosting regional green innovation. Based on provincial panel data from China from 2016 to 2021, this study employs the SBM-DEA model to construct a regional green innovation index, exploring the impact of national audit informatization on regional green innovation and its underlying mechanisms. The findings reveal that the informatization development of national audit significantly enhances regional green innovation. Mechanism analysis indicates that this improvement is primarily achieved through two pathways: increasing the efficiency of local government fiscal expenditures and optimizing regional industrial structures. Heterogeneity analysis further demonstrates that this effect is more pronounced in regions with higher levels of digital economic development, stronger rule of law, and better educational attainment. This research helps clarify the pathway from “macro-level national governance-local government behavior-regional green innovation”, linking macro governance to microeconomic outcomes. It provides valuable insights for local governments to explore green regional development policies from the perspective of national audit.