Taking the soil composite erosion process of Haifeng karst basin in eastern Yunnan province as the research object, the distribution characteristics of comprehensive soil erodibility index (CSEI) were analyzed, and the correlation, variation trend and influencing factors of soil erodibility between surface and underground soil were discussed, so as to deeply understand the soil erosion mechanism in karst area and control rock desertification. Through field investigation and sampling, soil hydrometer, wet screening of aggregates and other methods, the physical and chemical properties and erodibility change characteristics of soils in different erosion fields on the surface and underground of karst fault basin in eastern Yunnan were analyzed. The results showed that: (1) Soil physical and chemical properties changed with the erosion process. Clay, SOC and large aggregate (>0.25 mm) in the soil showed a decreasing trend, while silt and small aggregate (<0.25 mm) showed an increasing trend. There were significant differences in soil characteristics among different erosion processes. The content of soil clay (20.91%~45.62%), sand (44.96%~64.59%), SOC (4.93~88.72 g/kg) and large aggregate (17.82%~99.86%) in surface erosion process was higher than that in underground leakage process (15.30%~30.86%, 43.63%~64.59%, 3.57~19.05 g/kg and 16.81%~85.94%). The content of silt (4.85%~30.84%) and small aggregates (0.14%~82.18%) was less than that of underground leakage process (16.03%~25.86% and 14.06%~83.19%). (2) CSEI was closely related to soil physical and chemical properties. CSEI was negatively correlated with clay, sand, large aggregates, SOC, MWD and GMD (p<0.01), and positively correlated with silt and small aggregates (p<0.01). The main influencing factors of CSEI were SOC and soil aggregates stability. Clay, sand, SOC and water-stable aggregate contents had greater influence on CSEI of surface erosion process, while other factors had greater influence on CSEI of underground loss process. (3) CSEI had applicability to evaluate soil erodibility in the process of surface and underground erosion in karst basin, the CSEI of underground leakage was higher than that of surface erosion, both of which rose with the change of erosion process and soil depth. And the underground leakage process had secondary erosion effect. The soil erosion process was a compound and continuous process of surface erosion and underground leakage. The synergistic restoration of vegetation-soil could enhance soil erosion resistance.