The innovative city pilot policy is a new engine to accelerate the social development of China, which is an important support feature for realizing sustainable economic development. Using the city pilot policy issued by the Chinese government in 2008 as a quasi-natural experiment and the method of multi-period difference-in-differences (DID) model, we explore the effect of the policy on regional carbon emission efficiency. The research shows that the innovative city pilot policy could lead a significant promotion of the carbon emission efficiency of cities, which shows the characteristics of dynamic sustainability, that is, the policy effect continues to increase over time. Mechanism analysis reveals that the innovative city pilot policy mainly drives the improvement of urban carbon emission efficiency through improving the green technology innovation level of pilot cities, promoting the upgrading of regional industrial structure and increasing government investment in science and technology. In addition, the innovative city pilot policy has a spatial spillover effect on urban carbon emission efficiency, that is, the innovative city pilot policy not only promotes the local carbon emission efficiency, but also improves the carbon efficiency of neighboring areas.