Abstract: Danjiangkou Reservoir is the water source of the middle route of South-to-North Water Diversion Project. Keeping the water quality in good condition is the key to ensuring the success of the project. In this paper, the high resolution remote sensing data was used as the data source to obtain the spatial distribution characteristics of karst rocky desertification in the water source area and reservoir area. Karst rocky desertification in the reservoir area was mainly distributed in Xichuan County, Henan Province, with a total area of 327.59 km2. The incidence rate was 23.11%, which was 5.7 times that of the water source area. Based on field investigation and geological characteristics, three typical modes of rocky desertification in the reservoir area were established according to the main controlling factors, which were rocky desertification caused by human activities, rocky desertification caused by natural conditions and rocky desertification caused by intensified human activities led by natural conditions. It was pointed out that for the rocky desertification in Danjiangkou Reservoir area, the geological setting was a material basis, the climate condition was a background, and the human activity was a dynamic source. The proposed mode of rock desertification characteristics and its cause can provide a basis for rock desertification control and ecological restoration in the reservoir area, and provide an important reference for the establishment of rock desertification cause modes in other karst areas.