National audit serves national governance, which is an important guarantee for the modernization of national governance. Its function is bound to have an important impact on the production and export behavior of enterprises and the quality of export products. Using the data of Chinese industrial enterprises, the data of import and export products of China Customs and panel data of Chinese cities, this paper empirically tests the impact of national audit governance on the quality of enterprises’ export products, and probes into its internal mechanism. The study finds that national audit governance can significantly improve the quality of export products of manufacturing enterprises by promoting technological innovation, improving production efficiency and correcting public financial expenditure preference. The results are still robust after replacing the core variables, eliminating the outliers and controlling the endogenous problems. The impact of national audit governance on the quality upgrading of export products has obvious heterogeneity. Based on the perspective of micro enterprises, this paper discusses the impact of national audit governance on the quality of enterprises’ export products, which not only helps to provide more reliable micro evidence for promoting the effectiveness of national audit, but also has important practical significance for improving the competitiveness of enterprises’ export trade and promoting the transformation and upgrading of enterprises.