Alpine wetlands and meadows across the Three Rivers Source Region (TRSR) store high soil organic carbon (SOC). However, information on factors affecting SOC storage is scanty. Herein, we investigated SOC storage and explored factors affecting SOC storage, including climate, soil properties and above‐ and belowground biomass, using 50 soil profiles across the TRSR on the Tibetan Plateau. The SOC storage was 491.9 ± 158.5 Tg C and 545.2 ± 160.8 Tg C in the TRSR alpine wetlands and meadow, respectively. The SOC stock was positively correlated with the mean annual precipitation. However, no significant correlation between SOC stock and mean annual temperature was observed, as opposed to the global trend. In addition, SOC stock was positively correlated with both the aboveground biomass (AGB) and belowground biomass (BGB). Soil pH indirectly affected SOC stock, while SOC stock positively correlated with Al and Fe oxyhydroxides. Compared with vegetation biomass and climatic factors, soil properties, including soil pH and Al and Fe oxyhydroxides (Alo and Feo), affected not only SOC stock variation but also affected the impact of vegetation and climatic factors on SOC stock. Climate factors, AGB, BGB, soil pH, Alo and Feo jointly accounted for 59% of SOC stock variation in alpine wetlands and 64% of SOC stock variation in alpine meadow. This study suggests that soil properties are the dominant factors affecting SOC variation in alpine wetlands and meadow on the Tibetan Plateau.