Rock fragments can alter soil structure, thus profoundly affecting soil properties, hydrological and erosion processes. Hence, it is essential to quantify the role of rock fragments in soil-water processes in order to fully grasp their complex impacts on soil erosion. In this study, the effect of vertical embedded (VE) and covered (CV) rock fragments on runoff and soil loss of sloping cropland were investigated in plot scale through field monitoring experiments, with bare land (CK) as a control. Results showed that surface runoff from VE decreased by 24.93% compared to bare land, while subsurface flow and underground flow increased by 12.47% and 10.85%, respectively. Similarly, compared to bare land, CV decreased surface runoff by 14.08% and increased subsurface flow and underground flow by 7.09% and 7.29% respectively. Consequently, both VE and CV effectively decreased surface runoff and enhanced the proportion of rainwater converted into subsurface flow and underground flow (P < 0.05). Simultaneously, the benefits of VE in reducing surface runoff and promoting rainwater infiltration was found to be more significant than that of CV (P < 0.05). In terms of soil erosion, compared with bare land, VE reduced the surface soil loss rate by an average of 41%, while CV instead increased the surface soil loss rate by an average of 3.64%, and these changes were both statistically significant (P < 0.05). Moreover, soil erosion from subsurface flow and underground flow may be a long-term accumulation process, resulting in insignificant differences in soil erosion rates between treatments in this study (P > 0.05). Therefore, in studying the impact of rock fragments on soil erosion in karst sloping cropland, the focus should be on soil erosion caused by surface runoff. Additionally, the impact of rock fragments on the transformation of rainwater and soil erosion was limited by rainfall conditions, with VE showing a more prominent effect in preventing soil erosion under heavy rainfall conditions. Overall, the impact of rock fragments on soil erosion varies depending on their distribution patterns in the topsoil. It is necessary for these differences to be incorporated into process-based runoff and erosion models.