Alpine meadow is important for carbon (C) sequestration. Under cold and humid circumstances, the decomposition of soil organic matter is relatively slow, and thus soil C accumulation plays crucial roles in maintaining regional C balance. However, soil degradation of alpine meadow is extremely sensitive to anthropogenic activities. The study on the response of soil C pools to herding can provide scientific basis for deepening the mechanism of alpine meadow degradation. Pig uprooting is one of the major herding forms at the altitude of 3 000-4 000 m in China. In this work, the northwestern plateau wetland (Napahai) was selected as the study area, and the differences in soil C pools between yak tramping and pig uprooting on alpine meadows in Napahai was analyzed. The results showed that the pig uprooting reduced the total organic C and labile organic C (highly labile organic C, medium labile organic C, and low labile organic C) when compared to the yak tramping. The medium labile organic C is the most sensitive to pig uprooting among all studied C pools, and thus can be used as an important ecological indicator for soil disturbance. The soil microbial biomass C under pig uprooting was lower than that under yak tramping. Along with increasing soil depth, soil C storage decreased, and its response to herding disturbance also decreased. While, topsoil (0-10 cm) was the most affected by herding. In different study areas, due to the distinct soil physical and chemical properties, soils in terrestrial meadows showed a greater response to pig uprooting when compare to swamp meadows. Redundancy analysis (RDA) further indicated that soil C pools was closely related to soil water content, bulk density, porosity and so on. Overall, the changes in soil C pools were associated with herding patterns, regions, and soil depths. Pig uprooting led to soil bareness and structural changes, which resulted in a significant decrease in soil organic C, thus may lead more severe damages to ecosystems when compared to yak tramping.