Karst water is an extremely important resource and can respond to precipitation events quickly due to the high rock exposure rate, shallow and uneven soil layers, and various crack sizes. The impacts of this special rock-soil structure type on hydrological processes are difficult to quantify, mainly because the karst subsurface structure is very complex. In this study, lysimeters representing four rock-soil structures with two rock exposure rates (50% and 80%) and two soil thicknesses (5 cm and 20 cm) were constructed at the Puding Karst Ecosystem Research Station, Chinese Academy of Sciences. The following results were obtained by observing the evaporation and leakage from September 2019 to August 2020. 1) Over a year, the evaporation of the 80% rock exposure lysimeter was approximately 8% less than that of the 50% rock exposure lysimeter, while the two lysimeters with different soil thicknesses had only a 2% difference in evaporation. 2) The surface evaporation of different rock exposure rates varies greatly after different rainfall intensities. However, there was no significant change in surface evaporation between different soil thicknesses after rainfall of different intensities. 3) Generally, with the increase in the rock exposure rate, the infiltration coefficient nonlinearly increased. The leakage coefficients for cracks of different sizes and different soil thicknesses were approximately 0.67 and 0.57, respectively. 4) The amount of leakage and the time to reach the peak flow varied greatly among different rock-soil structures and were also affected by the antecedent rainfall. Thus, rock exposure has a great impact on surface evaporation after rainfall, and the influence of cracks on subsurface hydrological processes was greater than that of soil thickness. These findings can provide a scientific reference for water use and management practices in karst areas.