[Objective] The differences of soil erosion between micro-topography, microhabitat in clear-cutting site of the karst region were studied in order to provide suggestions for ecological restoration and control in clear-cutting site of the karst region.[Methods] Soil erosion monitoring method of pin was employed to monitor annually soil erosion in situ (differentmicro-topography, microhabitat) at a distance of 1 m×1 m within a research area enclosed by iron bars, and box chart and significance test were utilized to compare the difference of soil erosion between them.[Results] It was found that significant difference in the degree of soil erosion of different micro-topography and microhabitats in the study area. More specifically, depth of soil erosion of micro-topography manifested an overall scale of convex > flat > concave, while depth of soil erosion of microhabitat demonstrated an overall scale of stone-drain > stone soil surface > the side of stone > soil surface > rock tunnels. There was a significant correlation between micro-topography and soil erosion, while no significant correlation existed between microhabitats and soil erosion in groups, but stone-drain and soil surface were respectively correlate to each other significantly.[Conclusion] Ecological restoration and control should be carried out according to different micro-topography and microhabitat in karst mountain clear cutting site, and the key of control lied in the convex micro-topography, the microhabitat of stone-drain and stone soil surface.