The relationship among topographic factors, human disturbance, and rocky desertification in karst areas was quantitatively assessed. A rocky desertification information database was established for the Houzhai River Basin and analyzed using grid-sampling and field observation. Rocky desertification affected a total of 14.43 km², and affected multiple land use types, including uncultivated lands, sloping croplands, arbor forestlands, arable land, shrub lands, shrub grass-lands, grasslands, abandoned lands, garden lands, arbor-shrub mixed forestlands, paddy lands, and artificial fruit forestlands. The rock exposure rate and soil thickness were mainly restricted by slope gradient, slope position, and human disturbance. Otherwise, human disturbance is subjective, mainly in areas with low rock exposure, thick soil, and gentle slope gradient. Uncultivated lands and abandoned lands accounted for 32.64% of the rocky desertification area, and there was a greater risk rocky desertification under these types of land use. A regression model revealed that the degree of human disturbance directly affects both rock exposure rate (negative effect:-0.286) and soil thickness (positive effect:0.264). However, only insignificant effects were observed for slope direction on either rock bareness (positive effect:0.067) or soil thickness (negative effect:-0.054). According to these findings, rocky desertification in karst mountainous basin can be easily remedied by, understanding its relationships with topography and human disturbance.