The paper overall thought the three factors such as support index, pressure index and coordination index and built the assessment model of water resources carrying capacity based on set pair analysis.Taking 16 Cities and autonomous prefectures of Yunnan Province for examples,it selected seven representative indicators that affect the carrying capacity change of water resources, used the set pair analysis and entropy method to evaluate the carrying capacity of regional water resources because of the uncertainty of indicators.The results show that the carrying capacity of Yunnan regional water resources is in good condition.Most of the areas have a surplus of water and have great value of development and utilization. In those more developed areas, the conflicts between people and water is more serious.The differences of carrying capacity of water resources between region are mainly influenced by the local socio-economic development level and demographic factors.The assessment model of water resources carrying capacity based on set pair analysis can effectively assess the carrying capacity of water resource in high land.Result shows that the method has the advantages of objectivity, comparability and fairness, calculation method is simple and effective ,and evaluation outcome is visual.