【Objective】The highly heterogeneous soil-rock structure in the karst area of Southwest China affects the soil hydrological process. Clarifying its controlling effect and driving factors on soil moisture is of great significance for understanding the regional hydrological cycle and improving the ecological governance of rock desertification. 【Method】Taking two typical lithologies (limestone and dolomite) as the research objects, this study designed 12 simulated soil tanks with different soil-rock structure. Based on soil moisture data (at 10, 20, 40, 70, and 100 cm soil depths) and meteorological monitoring data (precipitation, temperature, and humidity) from the hydrological year spanning March 2023 to February 2024, this study employs statistical analysis and fitting methods to investigate the characteristics of soil moisture variation across different soil-rock structures. It further examines how soil moisture content differences are influenced by both soil-rock structure characteristics and meteorological factors.【Result】The results showed that the fluctuation of soil moisture in different karst soil-rock structure decreased with the increase of soil depth; the soil moisture (11.07~43.21%) and coefficient of variation of each limestone soil-rock structure in the rainy period were higher than those in the dry period, the soil moisture in the 40~70 cm soil layer was the lowest while the storage in the 100 cm layer was relatively high, and the soil water storage was jointly controlled by the soil-rock ratio (negative correlation) and the thickness of the surface soil layer (positive correlation), with the fitting formula Z=-24.48X+0.88Y+100.47 (R2=0.9328) ; the soil moisture of dolomite was concentrated and lower than that of limestone, the average value in the rainy period (18.36~28.70%) was slightly higher than that in the dry period (15.10~25.53%), the coefficient of variation in the dry period was higher, and the soil water storage increased exponentially with the increase of soil thickness, with the fitting formula Z=13.85e(X/12.70)-13.26 (R2=0.9958) ; the soil water storage of limestone was significantly correlated with precipitation and relative humidity, while dolomite was only significantly correlated with relative humidity.【Conclusion】This study reveals the regulatory mechanism of lithology difference-dominated soil-rock structure on the variation characteristics and storage of karst soil moisture, clarifies that soil-rock fabric is a key factor in karst soil hydrology research, and provides data support and theoretical reference for regional eco-hydrological research and rock desertification governance.