Promoting the realization of sustainable development goals is an important aspect of the national audit’s work. In practice, the digital transformation of the national audit, which emphasizes the integrated development of digital technology and traditional auditing methods, has emerged as a significant tool for advancing regional sustainable development. Based on the quasi-natural experiment of the establishment of a national audit digital department, the impact of national audit digital transformation on the effectiveness of regional sustainable development and the mechanisms through which it operates is empirically tested in this study. The findings reveal that national audit digital transformation significantly promotes regional sustainable development. A mechanism analysis indicates that national audit digital transformation promotes regional sustainable development by improving the performance of the government’s environmental governance and corporate green innovation. A heterogeneity analysis further demonstrates that the positive effects of national audit digital transformation on regional sustainable development are more pronounced in regions characterized by a high reliance on secondary industries, intense government competition, and elevated public concern for environmental issues.