As exposed bedrocks commonly interface with the soil directly, lacking a transition layer, cracks at rock-soil interface cracks (RSI-Cracks), are well-developed, particularly following wet-dry alternation in karst critical zones. However, inadequate understanding of the influence of RSI-Cracks on multi-path runoff generation around bedrocks has hindered an in-depth comprehension of subsurface-dominated hydrological processes in karst areas. To address this gap, we developed micro-slope models replicating rock-soil interfacial configurations by building upon field investigations. Two conditions, namely, the presence and absence of RSI-Cracks, were incorporated, with rain intensity and rock surface inclination as experimental conditions. Our results indicate that RSI-Cracks significantly alter the runoff output (p < 0.05), exacerbating subsurface water leakage. Compared with that on slopes without RSI-Cracks, the proportion of surface runoff on slopes with RSI-Cracks is reduced, with a reduction range of 4 to 46%. Conversely, RSI-Cracks promote an increase in the proportion of outflow at the rock-soil interface (RSI flow), with an increase range of 7 to 38%. This is an important reason for the aggravation of subsurface water leakage through RSI-Cracks. However, there is no significant change in the water loss caused by internal soil seepage on slopes with or without RSI-Cracks. These findings provide novel insights into underground water loss, with valuable implications for the construction and improvement of hydrological models in karst areas.