The establishment of national ecological civilization pilot zones is an important step for China to explore the path of low-carbon and green development in the new stage of development. This study examines the impact of the construction of these pilot zones on the carbon productivity of the provinces where they are located, analyzes underlying factors, and provides evidence and experience for green and low-carbon development and ecological civilization construction in other regions. However, there is currently limited research on the carbon productivity of national ecological civilization pilot zones, especially a lack of in-depth analysis of their influencing factors. Using panel data on carbon productivity and other variables from 29 provinces in China (excluding Tibet Autonomous Region, Hainan Province, Hong Kong, Macao, and Taiwan) from 2004 to 2020, this paper analyzes the trends in carbon productivity among different provinces and investigates whether the construction of national ecological civilization pilot zones has improved the carbon productivity of the pilot provinces. The paper also further analyzes its influencing factors through empirical tests using regression control methods. The results show that carbon productivity in various provinces and cities in China has been increasing in recent years, with the growth rates of Fujian, Jiangxi, and Guizhou provinces higher than the average of the other 26 provinces. The difference became even more pronounced after policy implementation, and the conclusion remained valid after a comparative analysis with similar control provinces. The establishment of national ecological civilization pilot zones has significantly improved the carbon productivity of the pilot provinces, and this conclusion still held after robustness tests using time-placebo checks, other policy interferences, and information criteria for selecting optimal subsets. Further analysis of its influencing factors revealed that the pilot provinces had improved carbon productivity by optimizing their energy structure, promoting technological progress, and increasing labor productivity. Compared with the existing literature, this paper focuses on the first batch of pilot provinces of national ecological civilization pilot zones in terms of research objects, and studies the impact of the establishment of national ecological civilization pilot zones on the carbon productivity of the pilot provinces, which enriches and expands the relevant empirical studies of national ecological civilization pilot zones and provides experiences and suggestions for the construction of ecological civilization in China. In terms of methodology, this paper adopts a counterfactual research approach and uses regression control methods for empirical testing. This method is particularly suitable for samples with a small number of pilot objects and can yield more accurate empirical results. This study shows that the establishment of national ecological civilization pilot zones significantly improves the carbon productivity of the pilot provinces, and this policy effect is sustainable. The pilot provinces have improved carbon productivity by optimizing their energy structure, promoting technological progress, and increasing labor productivity. Therefore, the construction of national ecological civilization pilot zones should be further promoted to provide replicable empirical evidence for green and low-carbon development in other regions.