The Fourth Plenary Session of the 20th Central Committee of the Communist Party of China pointed out that during the “15th Five-Year Plan” period, economic and social development should adhere to the principles of high-quality development, comprehensive deepening of reform, and combining an effective market with a capable government. National audit is an important component of national governance, and as an important institutional arrangement for promoting good governance, it has a natural unity with macroeconomic governance. Building upon General Secretary Xi Jinping’s important statement that “the ‘second half’ of audit rectification is just as important as the ‘first half’ of problem identification, and the two must be advanced in tandem”, this paper further highlights the role of audit rectification. It innovatively constructs a measurement system for the “the first half” and “the second half” of national audit, integrates the state’s requirements for an effective market and a proactive government, and utilizes provincial panel data from 2009 to 2023 to examine the impact of national audit on high-quality economic development. The study finds that national audit has a significant positive impact on high-quality economic development. Mechanism analysis indicates that national audit can effectively empower high-quality economic development through the market environment and government governance as key intermediary pathways. Heterogeneity analysis reveals that differences in the stage of high-quality economic development, geographical location, urban tier, and the intensity of national audit oversight exert heterogeneous effects on the ability of national audit to empower high-quality economic development. Further research indicates that, at the current stage, national audit and local digital development levels have not yet formed an effective synergy, limiting the full realization of their combined effects. The study’s conclusions can serve as a reference for enhancing the supervisory effectiveness of national audit, aligning audit practices with their institutional status, and promoting the achievement of high-quality economic development goals.