The ecological compensation mechanism serves as an important institutional instrument for China to advance ecological civilization construction and coordinated regional development. From the analytical perspective of the national audit system and grounded in the theories of public accountability and law-based national governance, this study systematically constructs an analytical framework concerning how national audit leverages its functions to adapt the ecological compensation mechanism, and reveals the structural function of audit in the transformation of the compensation system from a policy instrument to a law-based governance institution. Through embedded supervision and evaluation in key links such as the formulation of compensation standards, national audit facilitates the ecological compensation mechanism to achieve rationalized standards, accountable fund utilization, evidence-based performance assessment, standardized procedures and law-based accountability, thereby forming a five-fold institutional adaptation path centered on evidence rules, procedural rules and liability rules. This path not only helps optimize the allocation structure of “rights, liabilities and interests” within ecological compensation, but also provides an institutional fulcrum for the in-depth integration of the compensation mechanism with the public fiscal accountability system, the natural resource asset management system and the legal system for ecological civilization.