To explore the impact and mechanism of low-carbon city pilot on the green efficiency of industrial water resources, this study utilizes panel data from 248 prefecture-level and above cities from 2005 to 2020. The green efficiency of industrial water resources in these cities is measured by super-efficiency SBM model. And empirical analysis is conducted by establishing a progressive DID model and a mediation effect model. The results show that the low-carbon city pilot can significantly improve the green efficiency of industrial water resources, and this promotion effect is heterogeneous, especially for cities with high water resources endowment, cities with high carbon emissions and cities with non-old industrial bases. The low-carbon city pilot can improve the green efficiency of industrial water resources by forcing polluting enterprises to quit and promoting green technology innovation. The regulatory policy tools adopted by low-carbon pilot cities have a significant effect on the exit of polluting enterprises, while the incentive policy instruments have a significant effect on green technology innovation.