According to the current situation of regional water resources, 18 evaluation indexes were selected and an evaluation index system of regional water security was established, which includes four criteria levels: water resources, economic society, ecological environment, supply and demand. The index weight was determined by entropy weight method, and the water resources security evaluation method based on fuzzy set pair analysis was used to evaluate the water resources security situation of Xinjiang in 2016. The evaluation results show that the overall security of water resources in Xinjiang belongs to the basic security level, and the spatial distribution of Northern Xinjiang is better than that of southern and eastern Xinjiang. The evaluation results are generally consistent with the results of matter-element analysis and comprehensive index method, and the evaluation results are reasonable.