The growth and overlay of a large number of bryophytes in the broken soil patches between the exposed bedrocks of karst have an essential influence on the infiltration and runoff process between the exposed bedrocks and even the whole rocky desertification area. The purpose of this study is to explore the effects of moss on the infiltration and runoff of soil patches between karst exposed bedrocks and the processes of rainfall, runoff and infiltration transformation on slopes through rainfall experiments. The results showed that the slopes between the karst outcrops are dominated by subsurface and underground pore runoff. More than 50% of precipitation is lost through underground pores, with surface runoff accounting for only 1–17% of the total. Bryophyte overlay significantly reduced the initial runoff from subsurface and underground pore runoff, and advanced the steady-state time of runoff from subsurface and underground pore runoff, suggesting that bryophyte coverage may reduce the risk of soil erosion caused by short-duration rainfall. Eurohypnum has a significant inhibitory effect on percolation between exposed bedrock and reduces rainfall leakage from subsurface and underground pores. Thuidium has a strong intercepting effect on rainfall, significantly reducing the formation of surface runoff and the risk of surface soil erosion. Moss overlay has an essential role in soil and water conservation between karst exposed bedrock, and Eurohypnum and Thuidium can be considered as pioneer mosses for ecological restoration in the process of rocky desertification control and ecological restoration, which can effectively solve the serious problem of soil and water loss in karst rocky desertification area and improve the benefit of soil and water conservation in karst area.