Guizhou Province is located in the center of the karst region in southwest of China, its topography is dominated by mountains with deep river valleys, which makes it difficult for the development and utilization of water resources. So, improving water resources utilization efficiency is of great significance to the sustainable development of Guizhou Province. Here, a water resources evaluation index system was established based on three first-level indicators of water resources utilization, social economy and ecological environment. On this basis, with secondary indicators as slack variables, the super-efficiency DEA model (SE-DEA) was used to calculate the super-efficiency value of the first-level indicators, and the interval analytic hierarchy process (IAHP) is used to calculate the weight vector of the first-level indicators. Based on the super-efficiency DEA and IAHP methods, a comprehensive water resources evaluation model SE-DEA-IAHP was established, and the overall value of water resources utilization efficiency was obtained. The results show that the efficiency value of water resources utilization in Guizhou Province from 2015-2019 was low, which fluctuated dynamically around 1; in view of the first-level indicators, the social and economic IAHP weight value was relatively large, but the water conversion efficiency was not as high as expected, indicating that the rapid economic development brought some waste of water resources; taking into account the special karst geological conditions in Guizhou Province, the key to achieve sustainable development of water resources is to maintain a virtuous cycle of water resources, increase the corresponding economic management investment, optimize the industrial water allocation structure and improve the technical means of water utilization in Guizhou Province.