The improvement of Green Total Factor Productivity (GTFP) is a crucial approach to realizing high-quality economic development. Based on the panel data of 284 prefecture-level cities in China from 2010 to 2017, a multi-period difference-in-differences model is constructed to empirically examine the promotional effect of Accountability Audit of Natural Resource(AANR) on improving GTFP. The results show that compared to non-pilot cities, there is a significant increase in GTFP in pilot cities where such audits have been implemented. Further research has found that AANR has improved GTFP by promoting green innovation. Digital technology can enhance the policy effect, and the higher the level of urban economic development or the less fiscal pressure, the more obvious the policy effect. The research conclusions not only provide empirical evidence for natural resource asset audit to promote high-quality economic development, but also provide theoretical support and policy basis for continuously improving urban GTFP.