Low-carbon transformation development is the only way to achieve the goal of “dual carbon”. In order to explore the path of national audit to promote low-carbon transformation, this paper uses the panel data of 283 prefecture-level cities as samples, builds a multi-time point difference model, and tests the impact of pilot audit of leading officials’ natural resource assets on the development of low-carbon transformation. The study found that the audit pilot can improve low-carbon transformation by promoting industrial structure upgrading, reducing the proportion of coal energy consumption, promoting green technology progress, and protecting forest and grass resources. Further analysis shows that the impact of pilot audit on the development of low-carbon transformation has a spatial spillover effect, and in regions with higher independence of government audit, regions with supervisory backgrounds of audit institution leaders, regions with low-carbon policy implementation, and regions with high dependence on natural resources, the role of the pilot audit in promoting low-carbon transformation is more significant. The conclusion is helpful to the construction of audit evaluation standards for outgoing officials’ natural resource assets under the goal of “dual carbon” and also provides necessary empirical support and policy notes for national audit to promote the development of low-carbon economic transformation in China.