•Subsurface runoff dominates the runoff components in karst hillslope.•Thinner soils decrease surface runoff and increase subsurface runoff.•Bedrock topography controlled subsurface runoff generation in the thinner soils.•Thinner soils had a higher contribution of new water than that in the thick soils. Hydrological processes in the critical zone are closely related to the soil–bedrock structures. However, the effect of soil thickness on the rainfall-runoff relationship on the hillslope with complex topography remains unclear. Surface runoff, lateral subsurface runoff from soil–epikarst interface, and epikarst runoff from the epikarst–bedrock interface were monitored on two adjacent plots with deep and shallow (66.0 vs. 35.4 cm) soil thicknesses from June 2019 to December 2020 in the karst region of southwest China. During the monitoring period, surface and subsurface runoff account for 20% and 37% of the total runoff in the deep-soil plot (DSP), and 3% and 43% in the shallow-soil plot (SSP). This demonstrates that runoff from the soil-epikarst system is predominant compared to the relatively small contribution of surface runoff. In the SSP, the surface topography wetness index (TWI) was highly coupled with bedrock TWI, and the bedrock TWI had a significant negative linear relationship (p < 0.01) with subsurface runoff. Moreover, isotope hydrogen-separation results showed that subsurface and epikarst runoff were dominated by pre-event water, but a higher contribution of event water was observed in the SSP than in the DSP. These findings supported the hypothesis that rainwater could infiltrate the epikarst more easily in shallow soil slopes. Rainfall and surface runoff exhibited a linear relationship in the dry season and a non-linear relationship in the rainy season, indicating the occurrence of threshold rainfall–runoff behavior. The rainfall amount threshold for surface runoff was higher in DSP (44.7 mm) than in SSP (39.5 mm), and the corresponding variation of rainfall intensity interpretation was greater (54% vs. 38%). For subsurface runoff, the rainfall amount threshold was higher in the DSP than in the SSP (91.0 vs 79.4 mm), and the corresponding variation of soil moisture interpretation was higher (56% vs. 20%). This demonstrated that runoff can be better predicted at deeper soil hillslopes by rainfall and antecedent soil moisture. Accordingly, this study emphasizes the importance of evaluating the spatial heterogeneity of soil thickness in hydrological process research.