As a crucial component of the national governance system, the role of national audit in urban carbon emission reduction has become increasingly prominent. The panel data of 255 prefecture-level cities in China from 2006 to 2019 was taken as a research sample, and the impact of national audit on urban carbon emission reduction was discussed. Results show that national audit fulfills three functions, identifying ailments, treating diagnosed ailments and preventing potential ailments, effectively reducing carbon emission intensity and enhancing carbon emission efficiency. Mechanism test shows that through enhancing government transparency, alleviating resource misallocation, and improving administrative management systems, national audit can significantly promote urban carbon emission reduction. Heterogeneity analyses revealed the carbon emission reduction effect of national audit under different scenarios from two dimensions of location factors and economic factors. Moreover, a policy substitution effect exists between national audit and environmental regulation, which allows national audit to mitigate the deficiencies associated with the absence of regional environmental regulation. Secondly, The quadratic term of national audit was introduced into the research to verify the existence of non-linear relationship between national audit and carbon emission efficiency, which provides more precise theoretical guidance for complex practices and the formulation of national audit policies. Lastly, the collaboration of various functions of national audit can create a “deterrent effect”, “resisting effect”, and “economic physical examination effect”, thereby effectively enhancing regional carbon emission reduction outcomes. These research conclusions confirm that high-quality audit supervision can effectively regulate and guide local government behaviors, translating institutional advantages into tangible governance efficacy, and thereby driving urban green transformation and low-carbon development.