In this study, surface soil and underground leakage water and soil were monitored and sampled for analysis over 3 caves in rocky desertification area in Guizhou, to research the physicochemical properties of surface soil and cave leakage water and soil under different geological environments. Results indicated that severe surface rocky desertification led to strong connectivity in fissure conduits of karst and large variation in drip rate of underground leakage water and soil, together with low clay content in leakage soil; pH and element contents became higher with more severe rocky desertification under the same lithology condition; mean values of Ca2+, Mg2+, and Sr2+ in leakage water were 31.48 mg/L, 17.65 mg/L, and 0.026 mg/L in Shijiangjun Cave, 58.39 mg/L, 2.49 mg/L, and 0.074 mg/L in Hanjiachong Cave, and 38.29 mg/L, 25.33 mg/L, and 0.037 mg/L in Rongfa Cave, respectively; the concentration of Mg2+ was low and those of Ca2+ and Sr2+ were high in Hanjiachong Cave for the influence of lithology difference, while the concentrations of Ca2+, Mg2+ and Sr2+ in leakage water of Rongfa Cave were higher than those of Shijiangjun Cave, which was influenced by weather condition; pH and element contents in leakage soil were higher than those in surface soil, which was the result of long-term chemical erosion of cave leakage water to leakage soil.