[Objective] This paper studied the regional difference and dynamic evolution of eco-efficiency in Fujian Province under the constraint of resources and environment, so as to provide theoretical support for a comprehensive understanding of the regional differences and dynamic evolution process of ecological efficiency in different regions of the province.[Methods] From the perspective of intrinsic traits of resource and environment in Fujian Province, using quantitative statistical methods, with the help of DEA-BCC and DEA-Malmquist index model, the panel data of 9 cities in Fujian Province from 2006 to 2015 were dealt with to illustrate technological progresses of eco-efficiency change index, including the variations of comprehensive technical change index, pure technical efficiency and scale efficiency index of total factor analysis.[Results] In the 9 cities, 4 regions in Fuzhou, Xiamen, Putian and Ningde area had reached their optimal DEA efficiencies. There were regional differences in eco-efficiency among different regions, and the eco-efficiency in coastal areas was significantly higher than that in inland ones.[Conclusion] It is concluded that the annual average ecological efficiency was decreasing. The change of technological progress was the main driving force leading to the change of TFP. The coordination between production management and technological progress needs to be strengthened step by step.