Scientific assessment provides important tools for the sustainable use of water resources. This paper applies the set pair theory of entropy weight to evaluate the uncertainty involved. A preliminary classification of samples is conducted by calculating the connection degree of each evaluation index, and then uniform, differential and confrontational analyses of set pairs are carried out on the samples to identify their level. In identifying the weight of each evaluation index, the entropy value theory of information theory is introduced into the model. Combined with Tarim 2004 to 2007 water resource data, an evaluation of the sustainable water resource utilization in this region is made from the social and economic, water resource and ecological environmental water resource evaluation index system. The results show that the development and utilization of water resources in the Sanyuanliu region of Tarim are saturated, and the utilization of water resources in the Hotan region (III), Aksu region (III) and Kashgar region (III) appears to be unsustainable. After a comparison with other methods, it is concluded that the evaluation result provided by the method is reasonable and objective.