In order to measure the coordination degree of economic, social and ecological development of Yunnan Province, an evaluation index system for water resources carrying capacity covering water resources, ecological environment, economy and society subsystems was constructed for the evaluation of comprehensive development and utilization of water resources in Yunnan Province. Here, the CRITIC-VIKOR method was used to comprehensively evaluate the carrying capacity of water resources in Yunnan Province from 2004 to 2018 and in the cities and prefectures of Yunnan in 2018. The results demonstrate that the comprehensive carrying capacity of water resources in Yunnan Province has increased slightly and still has the potential for improvement from 2004 to 2018, the carrying capacity of water resources and ecological environment subsystems have increased significantly, and the economy and society subsystem is the most stable and shows obvious room for improvement. In 2018, the comprehensive carrying capacity of water resources in Honghe Prefecture, Puer City, Lijiang City, Yuxi City and Dali City ranked the top five, and the comprehensive water resources carrying capacity evaluation values were 0.057 5, 0.101 9, 0.113 3, 0.207 6 and 0.281 5 respectively; whereas the comprehensive carrying capacity of water resources in Nujiang Prefecture, Lincang City, Zhaotong City and Baoshan City ranked the last four, and the evaluation values were 0.634 5, 0.814 4, 0.908 1 and 0.918 2, respectively. This study has important guiding significance for the comprehensive development, utilization and protection of water resources in Yunnan Province.