Soil aggregate is a basic unit of soil structure. The physical isolation of soil aggregate is the most important mechanism for soil to protect organic carbon from being decomposed by microorganisms. The effects of soil aggregates to maintain the stability of soil organic carbon even exceed the decomposability of organic carbon itself. Meanwhile, the distribution of organic carbon in soil aggregates and the stability of soil aggregate are closely related to the magnitude and stability of soil organic carbon pool, thus they can explain the change in soil organic carbon pool under the changing environment. Zoigê wetland, the most typic plateau wetland in the world, is the birthplace of the Yangtze and Yellow Rivers and stores a large of soil organic carbon. Since the 1960s, the Zoigê wetland has undergone extensive degradation which led to the decomposition of peat and the acceleration of carbon release. However, there are few research on the changes in organic carbon distribution in soil aggregates and its relationship with the changed soil organic carbon pool under alpine meadow degradation. Therefore, we investigated the soil organic carbon (SOC), soil aggregate, and aggregate-associated organic carbon in an alpine meadow and its adjacent degraded sites under the degree of light degradation (LD), moderate degradation (MD), severe degradation (SD), and extreme degradation (ED) in the Zoigê Plateau to explain the mechanism of soil organic carbon pool change and support for the restoration and management of alpine meadow. Wet sieving was used to analyze soil aggregate. The results showed that 1) the aggregate stability and the mass proportion and internal composition of the macroaggregate decreased with degradation, 2) the OC concentration of all size aggregate particles and internal fractions of macroaggregate also decreased with degradation, 3) although the OC stocks in free microaggregate, occluded microaggregate and occluded silt and clay increased with degradation, the decreased SOC was mainly resulted from the decrease of OC stocks in macroaggregate and coarse particulate organic matter, 4) in the surface soil (0-10 cm), the decreased SOC concentration was mainly due to the changes of OC concentration of microaggregate and macroaggregate, while it was the OC concentration of macroaggregate and the aggregate mean weight diameter (MWD) dominating the changes of SOC concentration in the subsurface soil (10-20 cm). Moreover, the SOC stocks in the 0-10 cm soil depth was largely affected by aggregate MWD, but that in the 10-20 cm soil depth was the result of the combination of aggregate structure, soil physicochemical properties and OC concentration of macroaggregate. Overall, improving the composition and stability of soil aggregates and increasing the macroaggregate-associated OC could increase the nutrient supply for plants and the SOC stocks, and ultimately could restore the productivity and function of the degraded alpine meadow.