Intense land degradation had created a special vegetation-soil-rock complex structure (VCS) on karst slopes, which altered regional soil and water processes. In this study, we investigated the combined effects of heterogeneous VCS on soil erosion/leakage, rainwater transformation and hydrodynamic characteristics at the microplot scale by simulating the karst dichotomous structure slopes with steel tanks and indoor artificial rainfall. The analysis showed that the surface runoff rate decreased with the increase of VCS and the subsurface runoff rate decreased with the increase of VCS. When the rainfall intensity increased to 60–120 mm/h, there was obvious surface runoff yield on the VCS slope. When the rainfall intensity exceeded 60 mm/h, the VCS showed obvious surface sediment yield with an initial rate ranging from 0 to 4.03 g·min−1. VCS showed obvious underground runoff and sediment yield under different rainfall intensities, and the initial rate was greater than 0.45 L·min−1 or 0.13 g·min−1. This suggests that soil and water leakage from the karst rocky desertification slopes may be generalized. All the erosion flow regimes of VCS slopes were rapid laminar flow or slow laminar flow. The drag coefficient and flow shear increased with the increase of VCS, and the flow power showed a trend of increasing, then decreasing and then increasing. The water flow shear and water flow power showed a power function relationship with the sediment yield rate (R2 ≥ 0.2293, P < 0.05). In terms of direct effects, hydrodynamic characteristics had the strongest influence on surface sediment yield (β = 0.68, P < 0.05), and rock exposure rate had the strongest influence on subsurface sediment yield (β = 0.56, P < 0.05). In terms of total effect, rainfall intensity was the dominant driver of surface/subsurface sediment yield (β = 0.75/0.72, P < 0.05). This study provides insights into understanding the mechanism of hydraulic erosion on rocky decertified slopes and provides a theoretical basis for decision-making on soil erosion management in karst areas.