Microhabitats, caused by the action of dissolution and soil erosion at different slope positions, are manifestations of rocky desertification in Karst areas of Southwest China. They play a significant role in the ecological restoration of the karst landscape by changing soil hydrological and soil erosion processes via affecting soil and vegetation properties as well as soil erodibility. Nevertheless, few studies have been conducted to investigate the potential influences of microhabitat types and slope positions on soil erodibility. Thus, this study was performed to assess the variations in soil erodibility indicators described by the soil cohesion (Coh), K factor (K), penetration resistance (PR), soil structural stability index (SSI), saturated hydraulic conductivity (Ks), and a comprehensive soil erodibility index (CSEI) at two slope positions (upper and lower) and four microhabitat types (rock pit, rock crevice, rocky soil surface, and soil surface). The results indicated that soil erodibility indicators of Coh, SSI, Ks, K, and PR varied significantly with microhabitat types and slope positions. Furthermore, CSEI varied from 0.45 to 0.77 and from 0.25 to 0.67 for the upper and lower slope positions, respectively. However, the microhabitat of rocky soil surface had the maximum CSEI, whereas the microhabitat of rock pit had the minimum CSEI for both slope positions. Furthermore, the mean CSEI among different microhabitat types of the upper position was dramatically greater than that of the lower position, indicating that the upper slope position was more prone to erosion in the karst region. All these variations in CSEI between different microhabitat types and slope positions were controlled by their influence on soil and vegetation properties. However, the influencing mechanism of microhabitat types on CSEI was completely different between these two slope positions. Changes in CSEI in different microhabitat types of the upper slope position were mainly controlled by the indirect effect of plant litter in promoting soil structure, whereas those for the lower slope position were regulated by the direct effect of plant root binding and bonding. These results have crucial implications for deeply comprehending the impacting mechanism of the spatial changes in soil erodibility under different microhabitat types and slope positions, particularly the impacts of rocky soil surface in the upper slope position on soil erodibility. Great attention should be paid to deploying biological measures for the microhabitat of rocky soil surface and the upper slope position, such as the cultivating of special biological soil crust, to prevent regional soil erosion and improve the environmental quality in karst areas of Southwest China. Soil erosion resistance; Microhabitats; Upper and lower slope positions; Soil and vegetation properties; Karst areas.