As a crucial factor of ecological environment, water ecological security pattern is a key component of ecological security pattern. Scientifically evaluating water ecological security situation, carrying out ecosystem management and protection have great significance to promote economic and social development. Taking 17 flow sections of Gansu province as the research object, the initial water ecological security evaluation index system was constructed based on the social-economic-compound ecological system (SENCE) concept, The system contains 33 indicators and is divided into four parts of economic development, social progress, natural resources, ecological environment. Combining fuzzy system analysis and improved niche theory, the initial water ecological security evaluation index system was optimized and the final optimized water ecological security evaluation index system consisted of 28 indicators. By the optimized index system to fuzzy comprehensive evaluation the water ecological security situation of the 17 flow sections in Gansu province from 2016 to 2018.The results showed that the proportion of water ecological security in the 17 flow sections with good condition was 35.3%, 41.2%, 35.3% from 2016 to 2018, respectively, the ratio of general condition was 57.8%, 52.0% and 46.1%, respectively,the proportion of the poor was 23.5%, 11.8% and 11.8%, respectively.The evaluation results were normally distributed,the inter-annual variation was small and the proportion was basically stable. The cumulative weight of such indicators as annual average precipitation, river-based flow, surface water supply, ecological environment water consumption, and water-saving irrigation area has reached 47.75%, These were the main factors affecting the water ecological security.