Addressing the unclear mechanisms underlying the influence of rock exposure in the surface-subsurface "dual" erosion structure of karst regions, this study employed indoor artificial rainfall simulation techniques to investigate the runoff and sediment yield characteristics and temporal variation patterns across the surface, soil interflow, rock-soil interface (RSI), and fissures under the influence of rock exposure rate, rainfall intensity, and slope. The results indicate that (1) The total surface runoff volume is positively correlated with rainfall intensity and rock exposure rate, whereas the sediment yield exhibits a nonlinear relationship with rock exposure rate, increasing initially and then decreasing (with a critical value of 20%). Runoff and sediment yield from underground fissures and the underlying RSI were significantly controlled by the rock exposure rate, exhibiting an inverse relationship. Surface runoff variation over time increased rapidly during the first 10 min before stabilizing or decreasing, whereas the sediment yield followed a V-shaped pattern. Subsurface runoff began to form and increased after 20 min, with the sediment yield generally showing a gradual or fluctuating increase. (2) No soil interflow was observed on the bare karst slopes with homogeneous soil. The runoff process at the RSI was positively influenced by rainfall intensity and slope, whereas the sediment yield exhibited a single-peak response to slope changes. (3) Importance analysis of influencing factors showed that rainfall intensity significantly dominated surface runoff and sediment yield processes (p < 0.05), rock exposure rate was the primary controlling factor for subsurface erosion processes, and slope primarily influenced sediment yield at the RSI. (4) Interaction analysis indicated that the interaction between rainfall intensity and rock exposure rate significantly affected the surface runoff and sediment yield. The research findings reveal the differentiated response mechanisms of the "dual" erosion structure in karst regions, providing a theoretical basis for regional soil and water conservation efforts.