In hilly agricultural landscapes with shallow soil, cultivation activities can cause the fragmentation of bedrock and induce vertical spatial heterogeneity of rock fragments, modifying the hillslope architecture and flow paths. Previous research mainly focused on the impact of rock fragments in the topsoil on surface runoff, but the role of subsurface rock fragments in rainfall-runoff processes has received less attention. In order to investigate the role of the subsurface rock fragment layer in rainfall-runoff processes through artificial rainfall experiments, we used sieved soil to establish soil layers with thickness of 10 cm and subsurface rock fragment layers related to hoeing depths from 10 to 16 cm under the soil layer. Additionally, a rubber plate was employed to initiate subsurface flow and deep percolation during the rainfall experiments. Results show that the presence of subsurface rock fragment layers mainly influenced the runoff partitioning between subsurface flow and deep percolation, but had little effect on surface flow. When there was no subsurface rock fragment layer, the yields of subsurface flow and deep percolation were in the ranges of 2.78-5.32 mm and 6.35-25.52 mm, respectively, under 15 degrees slope and 15-120 mm h-1 rainfall intensities. The presence of subsurface rock fragment layers resulted in a 30-110% increase of subsurface flow, compared with no subsurface rock fragment layer, and it resulted in deep percolation decreasing by 4-48%. Subsurface rock fragment layers with substantial thickness and content of coarse rock fragments facilitated runoff partitioning into subsurface flow, but reduced the fraction of deep percolation. Rainfall intensity and slope steepness both exerted positive effects on the magnitude of subsurface flow and deep percolation within the thresholds of 60 mm h-1 and 15 degrees, respectively. With increasing rainfall intensity (or slope steepness), subsurface flow yield increased apparently for the thick subsurface layer with substantial coarse rock fragments. It indicates that the thick subsurface rock fragment layer with high content of large-sized particles together with the great rainfall intensity (or steep slope) can result in substantial lateral subsurface flow. This study has important implications for the management of water and environment in hilly agricultural landscapes.