Exploring the coordinated development state of water resources and “social-ecological” system is an important measure to seek regional sustainable development. Based on the CA-Markov model and InVEST model, this paper analyzes the habitat quality of the Oujiang Basin in different periods. The evaluation index system of “water-resources-society-ecology” coupling system was constructed to evaluate the coordinated development of the Oujiang basin. The results showed that there were mainly high habitat quality areas in the Oujiang basin from 2000 to 2020, but the habitat quality level showed a downward trend, and the decline was further increased in 2030. The high quality area in the basin is concentrated in the southwest side. The areas with low habitat quality were mainly located in Longwan District of Wenzhou and near downtown Lishui City. The construction level and coupling coordination degree of “water resources, society and ecology” system are developing well, and the construction status of water resources subsystem is a key factor affecting the overall level. The improvement measures are proposed of guiding land use scientifically, rational planning of water resources allocation, optimizing the three aspects of industrial structure, in order to guide regional ecological protection and high quality development.