Alpine regions sequester large vulnerable and unprotected soil organic carbon (SOC), determining its extreme sensitivity to global change and pivotal role in the carbon cycle. However, there is ongoing debate regarding how SOC storage and its stabilizing mechanism vary along altitudinal gradients. Here, we examined the SOC contents of soil aggregate and density fractions, and their interactions with climate, biology, and soil properties along elevation (2100–3900 m) of western Yulong Mountain in Southwest China. Results showed that SOC contents in bulk soils and heavy fractions significantly increased with elevated altitudes, whereas no changes in aggregates. The increasing Fe/Al oxides with altitudes might be responsible for such significant variations. While soil C-enzyme activities had strong effects on increasing SOC in macroaggregates (> 250 μm), aggregate stability (indicated by mean weight diameter and soil erodibility) mainly reduced SOC in microaggregates, silt and clay (< 250 μm). The structural equation models further showed that 57%–91% of variations in SOC contents could be explained by environmental variables, with the Fe/Al oxides showing the strongest positive associations with SOC contents in bulk soils, light and heavy fractions. Taken together, our results emphasized positive impacts of mineral protection on the SOC stabilization at high altitudes. This not only offers novel insights into predicting soil C stability in alpine regions but also provides practical significance for soil C pool management across various altitudes.