In view of the characteristics of the integrated water system in small coastal watershed and the prominent characteristics of frequent flood and drought disasters, water ecology and water environment problems, a comprehensive evaluation index system of water ecological civilization in small coastal watershed was established, which includes six aspects of flood control safety, water supply safety, water environment, water ecology, water management, water culture and 29 individual indexes. A comprehensive evaluation method of water ecological civilization in coastal watershed based on cloud model was proposed. This method was used to evaluate the current situation of water ecological civilization in Xianghetan River Basin. The results show that this method can effectively identify the outstanding problems in the construction of water ecological civilization in small coastal watershed.