Based on the panel data of 110 prefecture-level cities in the Yangtze River Basin Economic Belt from 2010 to 2017, the implementation policy of the pilot audit of natural resource assets was taken as a quasi-natural experiment, and the multi-period DID model was used to evaluate the impact of the pilot policy of departing audit on the level of regional green total factor productivity. It is found that the outgoing audit of natural resource assets can effectively improve the level of green total factor productivity in the region. The policy effect of the natural resources leaving audit pilot in production varies in different regions, which is mainly reflected in the improvement of green total factor productivity in the upper and lower reaches of the Yangtze River Basin, but the impact on green total factor productivity in the middle reaches is not significant.