Alpine ecosystems potentially store a large amount of soil organic carbon (SOC), but they are highly sensitive to climate change. The assessment of SOC stabilization mechanisms in these ecosystems is therefore vital to understanding the C dynamics in terrestrial ecosystems. Here, we investigated the soil aggregate distribution, aggregate stability, and associated SOC contents within alpine forest and grassland soils along an elevation gradient (2600–3900 m a.s.l) in the Yulong Mountains of Southwest China. Our results showed that the SOC contents in bulk soils and aggregates were higher within grassland soils than in forestland soils, with higher levels in the topsoil (0–10 cm) than in the subsurface soil (10–20 cm) layers at each elevation. The large macroaggregates (>2000 µm) accounted for the largest proportions of aggregate fractions (50.54% and 49.11%) and contributed the greatest proportions of C (55.44% and 52.12%) to the whole soil C within forest and grassland soils, respectively. Generally, the proportions of large macroaggregates, microaggregates (53–250 µm), mean weight diameter, and geometric mean diameter increased significantly with increasing elevation across different soil depths and land types, suggesting that soil C stability was improved with increasing elevation. The SOC contents in bulk soils and aggregates also showed an increasing trend with increasing elevation, with the highest level observed at 3900 m within forestland and 3200 and 3900 m within grassland soils at both soil depths. Climate factors, soil factors, Al/Fe oxides, and aggregate stability indices interactively explained 86% and 52% of the variation in soil C within forest and grassland soils, respectively. Among them, the incorporation of the Al/Fe oxides increased the total explained SOC variations by approximately 10%, exceeding the SOC variations explained by climate or soil factors. Overall, our results provide useful insights into the patterns and mechanisms of soil C stabilization along elevation gradients in alpine ecosystems.