This paper takes the National Ecological Civilization Pilot Zone established in batches since 2016 as a quasi-natural experiment, and empirically evaluates the impact and mechanism of its construction on carbon emission efficiency in each pilot zone using the synthetic control method. The study reveals that the construction of the National Ecological Civilization Pilot Zone has helped to improve the carbon emission efficiency of both Fujian and Jiangxi, with a greater improvement observed in Fujian. The conclusion is still valid after placebo test, sorting test, sparse synthesis control test, and DID. Additionally, the efficiency decomposition find that the construction of the National Ecological Civilization Pilot Zone has improved the scale efficiency change index of carbon emission in Fujian and promoted both the scale efficiency change index of carbon emission and the pure technical efficiency change index of carbon emission in Jiangxi. Mechanism analysis further reveals that promoting green technology innovation and optimizing energy utilization efficiency can play a positive role in the construction of the National Ecological Civilization Pilot Zone to improve carbon emission efficiency as both endogenous and external means. Overall, this study provides theoretical references and policy recommendations for promoting the construction of ecological civilization in China and achieving the carbon peak and carbon neutrality goals as soon as possible.