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Soil organic carbon (SOC) is essential for ecosystem stability and long-term carbon storage in alpine grasslands, yet the relative importance and interactions of hydrothermal and biotic controls remain poorly understood at regional scales. In this study, we quantified surface SOC (0–20 cm) across the Yellow River Source Region (YRSR) on the northeastern Tibetan Plateau, a climate-sensitive alpine headwater system characterized by strong hydrothermal gradients and freeze–thaw dynamics. Field-based SOC measurements were integrated with multi-source remote sensing and reanalysis data that describe thermal conditions, moisture processes, vegetation productivity, soil properties, topography, and human influence. A two-step screening approach was applied using Boruta and variance inflation factor filtering, followed by modeling with random forest. The model outputs were interpreted using Shapley Additive Explanations (SHAP). SOC displayed significant spatial heterogeneity across the region. Vegetation productivity, moisture availability, and thermal conditions were identified as the dominant nonlinear drivers of SOC variation. Moisture processes were found to function as a central mediator, regulating SOC both directly and indirectly through vegetation and thermal pathways. These findings highlight the critical role of hydrothermal stability in sustaining soil carbon stocks and provide a quantitative foundation for sustainable grassland management strategies in the face of climate warming.