Environment-economy-society compound system is big complex system coupled by environment subsystem, economy subsystem and society subsystem, and the interaction and feedback mechanism between the inside of every subsystem and between every subsystem jointly keep the operation and development of the total system. The analysis based on 26 counties in Three Gorges Areas during 2005-2014 shows that the development level of the environment-economy-society compound system in Three Gorges areas is stably improved, trends to be health and coordinated but currently the coupling level is at low level, that the reservoir head and reservoir hinterland are the weak link for the coupling, and that in the future, the compound system will be coordinated at higher level. China should accelerate the process of green development, superogation and rationality of the industrial structure in the areas, the reservoir head and reservoir hinterland should stick to “protecting the important regions and developing important nodes”, the reservoir tail should “overall develop and holistically optimize”, the Three Gorges areas should set up and perfect the ecological compensation mechanism at whole basin, reconstruct big Three Gorges areas based on basin development so as to boost the coupling and coordinated development at higher level of environment-economy-society compound system in the areas.