<p>Soil organic carbon (SOC) plays a crucial role in the ecological stability of Semi-Arid Alpine Ecosystems and in the global carbon cycle. However, its dynamic loss mechanisms, particularly the synergistic effects of snowmelt and rainfall-induced erosion, remain unclear. This study focuses on the upper Heihe River basin in the central Qilian Mountains, China. Six types of erosion units were set up along an elevation gradient, and field surveys were conducted over two years. Based on the XGBoost algorithm, digital mapping of SOC at the basin scale was carried out. Using the 2006–2020 period as the simulation timeframe, a composite hydraulic erosion calculation method was developed by coupling the SPHY hydrological model with the RUSLE model, incorporating snowmelt runoff and observed sediment data. Geographic detectors and structural equation models were used to reveal the driving mechanisms of composite hydraulic erosion on SOC loss. The results showed that the SOC density in the 0–20&#xa0;cm soil layer of the basin was 10.90 × 10⁶ kg C m^− 2. The annual average soil sediment yield modulus in the basin ranged from 7.82 to 14.49 t ha^− 1 yr^− 1, with an SOC output rate of 0.50 ± 0.08 t C ha^− 1 yr^− 1. The total SOC loss in the basin was (50.16 ± 8.57)×10⁴ t C yr^− 1, with rainfall-induced erosion contributing 94% and snowmelt-induced erosion contributing 6%, highlighting the significant role of snowmelt erosion in future carbon management. High carbon loss areas were primarily concentrated in alpine cold deserts and alpine meadows, which accounted for 89.81% of the total SOC loss in the basin, making these areas key targets for future carbon management in semi-arid, high-altitude regions. The SOC loss rate during wet-cold years (0.62 ± 0.15 t C ha^− 1 yr^− 1) was 1.31 times and 1.51 times higher than in normal years (C2) and dry-hot years (C3), respectively, indicating the need for differentiated carbon management strategies based on climatic conditions. The coupling effects of composite hydraulic erosion processes under climate and topography regulation, along with the erosion-suppressing effect of surface vegetation, jointly determine the spatial heterogeneity of soil carbon loss. This study deepens the understanding of the water erosion–carbon loss process in semi-arid, high-altitude regions and provides theoretical support for erosion control and carbon management in alpine ecosystems.</p>