As a crucial carrier of natural resource and environmental information, the natural resources balance sheet is important in enhancing ecological governance capabilities and advancing ecological civilization construction. Utilizing panel data from Chinese prefecture cities spanning 2012 to 2018, we employ a Difference-in-Differences (DID) model to examine the policy effects of the natural resources balance sheet system. The findings indicate that compiling the natural resources balance sheet significantly promotes local ecological civilization construction, and local government environmental governance efficiency partially mediates this relationship. Further analysis indicates that the outgoing audit of natural resources and public environmental concern positively moderates the relationship between the two. Drawing on the principal-agent theory, we provide in-depth analysis and elucidation of the mechanisms through which the natural resources balance sheet promotes ecological civilization construction, offering theoretical guidance and empirical data support for strengthening the compilation and application of the natural resources balance sheet.