Independence is the soul of auditing. How to improve the independence of audit institutions is of great significance to the improvement of audit quality. Taking the pilot of “unified management of personnel, assets and property of the local audit institutions below the province” as a quasi natural experiment, selecting the audit institutions of prefecture level cities in China from 2013 to 2017 as the research sample, this paper empirically tests the impact of independence on the audit quality of local audit institutions. The empirical results show that the reform has significantly improved the audit quality of local audit institutions. Further analyses find this finding is more pronounced in eastern region, and regions with lower level of legalization and lower financial pressure. By conducting a series of robustness tests, the results remain unchanged. In this paper, we verify that the independence of audit institutions is of great significance to audit quality. The conclusions have important enlightening significance for continuing to deepen the reform of the audit management system.