As the first national ecological civilization pilot zone in China, Fujian Province has made significant progress, with a series of successful experiences in ecological civilization construction. This paper summarizes achievements in economic construction, environmental management, ecological protection, and human settlements construction since 2001 in Fujian Province. The authors find that the constraints on resources and on the environment are still considerable regarding future development in Fujian Province, and that the adaption of the institutional system to ecological civilization needs improvement. The authors also find that the conflict between development and ecological protection is becoming more and more prominent in the mountainous region of Minxi and Minbei. This paper summarizes the experiences gained during the top-level design, transformation from development mode, green governance, and system construction of ecological civilization in Fujian Province. The authors suggest that the national ecological civilization system reform pilot should be demonstrated intensively in Fujian Province, forming a strong institutional system that can lead the way in ecological civilization development and demonstrate its effects. The authors also suggest that Fujian Province should focus on promoting green economic transformation, innovating a supervisory system for the ecological environment, and optimizing the pattern of homeland security for the next stage of development.