The carrying capacity of water resources has a crucial impact on the sustainable development of a country or region. Taking the characteristics of the basin in the central Yunnan Plateau and the factors affecting the carrying capacity of water resources into account, 14 indexes are selected to establish an index system for evaluating the carrying capacity of water resources. Based on the theory of set pair analysis, the fuzzy set pair evaluation model is improved, and the principle of minimum information entropy is used to combine the subjective and objective weights of the AHP and entropy weight method to establish the fuzzy set pair evaluation model of water resources carrying capacity. For comparison, an improved fuzzy set evaluation model and a fuzzy comprehensive evaluation model were adopted respectively to evaluate the water resources carrying capacity of the Long chuan River Basin. The results show that the water resources carrying capacity of 5 years are all grade 2 by using the fuzzy comprehensive evaluation method, and the water resources carrying capacity of 5 years are respectively grades 2, 1, 2, 2 and 1 by using the fuzzy set pair evaluation method. Through the comparative analysis, it is concluded that the improved fuzzy set pair evaluation model is sufficient for the index information mining, and the calculation is simple. The evaluation results can provide a scientific basis for the further protection and management of the river chief system of water resources in the Long chuan River Basin.