Soil erosion, particularly inter-rill erosion, plays a critical role in the redistribution of soil organic carbon (SOC) and its associated fractions. However, the effects of rainfall kinetic energy (KE) on the dynamics of sediment and organic carbon loss remain poorly understood. This study investigates the influence of varying rainfall KE on sediment yield, runoff, particle size distribution (PSD), and SOC fraction loss during inter-rill erosion. To address these questions, micro-plots covered with iron mesh screens of varying apertures (1, 2.5, 5, 10, and 20 mm) were established to modulate rainfall KE, with a bare plot serving as the control. The objectives were to quantify the variations in sediment and SOC fractions in response to different rainfall KE levels, examine the relationships between rainfall KE and erosion parameters, and explore the mechanisms behind SOC fraction loss during erosion. The results indicated that increasing rainfall KE enhanced sediment and runoff yields, as well as sediment concentration, with a clear relationship between rainfall intensity, duration, and KE. PSD analysis revealed that the proportion of clay and silt initially decreased with increasing KE but later increased under higher KE, suggesting selective transport of fine particles as aggregates. Notably, SOC losses, including particulate organic carbon (POC) and mineral-associated organic carbon (MOC), decreased by 48.57% to 71.14% and 49.79% to 75.59%, respectively, compared to the control plot. MOC, the dominant fraction within SOC, was impacted by KE, both in terms of content and loss. Structural equation modeling (SEM) revealed that the loss of SOC fractions was primarily mediated by sediment yield, which was indirectly influenced by rainfall KE. Our findings highlight the complex interplay between rainfall KE, sediment dynamics, and SOC fraction transport during inter-rill erosion. This study contributes novel insights into the role of rainfall KE in shaping organic carbon distribution and provides a deeper understanding of erosion-induced carbon fluxes in the context of global carbon cycling.