The Chinese government proposed the establishment of China National Ecological Civilization Pilot Zone in 2016 to further explore the coordinated development of economy and environment, and Fujian, Jiangxi and Guizhou provinces were selected as the first batch of pilot zones. After years of exploration, it is necessary to discuss and summarize the construction progress of the three pilot zones from the perspective of the city. In this study, first, the ecological civilization pilot zone construction system was decomposed into an economic construction subsystem (ECS) and an environmental optimization subsystem (EOS). Then, a two-stage network SBM model was adopted to calculate the efficiencies of the subsystems, and the Kruskal-Wallis test was used to measure the efficiency difference. Finally, a panel data regression model was applied to explore the influencing factors of both subsystems. The results show that the ECS efficiency is higher than that of the EOS, and the ECS efficiency in Fujian is significantly better than that in Jiangxi and Guizhou, however, there is no significant difference in EOS efficiency in the three provinces. Furthermore, industrial structure and population agglomeration have a significant effect on ECS efficiency, environmental regulation has a significant impact on EOS, and the technology level has a significant impact on both subsystems. Based on the results, policy implications for improving the efficiency of the two subsystems were given respectively.