Abstract: Due to the unique above-ground and underground binary hydrological structure in the karst area, the karst water system has a special circulation evolution. So the water can not only carry the surface loss of the soil, but also the underground loss, resulting in large soil loss and karst rock desertification in the area. The phenomenon is outstanding and the governance is difficult. This paper takes the demonstration area of rocky desertification control in Huanjiang Gorge Plateau of Guizhou Province as the research area. Through field investigation, water sample analysis and numerical simulation method, the karst water system's recharge, runoff, drainage characteristics, water chemistry characteristics and water balance are analyzed and simulated to calculate the groundwater level and underground dark river flow changes. The equilibrium amount of karst water in this area is obtained. The results basically reflect the changes of actual groundwater system discharge and groundwater flow characteristics, and preliminarily clarify the cyclic evolution characteristics of the karst water system in this area. They provide a theoretical basis for the study and prevention of soil surface loss and underground loss in karst rocky desertification areas.