Unsustainable use and management of alpine pastureland for grazing and hay could reduce large pools of C stored in soils. We measured total organic C, total N, organic C associated with particle-size fractions, dissolved organic C and microbial biomass and activity at three soil depths under annual oats cultivated for hay for 28 years, introduced perennial pasture (8 years after establishment) and native pasture at an alpine site in western China.Compared with native pasture, the soil under annual oats had 26–42% lower total organic C and total N at different depths. In perennial pasture, total organic C and total N decreased by 10–18%, but only at 0–10cm depth. Native pasture contained 19, 6.3 and 4.1g of coarse organic C (0.1–2mm size) per kg soil at 0–10, 10–20 and 20–30cm depths, respectively. Corresponding amounts of fine organic C (0.05–0.1mm size) were 3.2, 1.9 and 1.3gkg −1 soil, and those of stable organic C (<0.05mm size) were 58, 56 and 54gkg −1 soil. Significant decreases in coarse organic C (by 58% at 0–10cm, 30% at 10–20cm and 66% at 20–30cm depths), fine organic C (by 42–47% across different depths) and stable organic C fraction (by 28% at 0–10 and 10–20cm depths and 38% at 20–30cm depth) were found in soil under annual oats relative to native pasture. In perennial pasture, coarse organic C decreased by 69% at 0–10cm, 21% at 20–30cm and 37% at 20–30cm depths, whereas fine organic C decreased between 69 and 78% across different depths compared with native pasture. Dissolved organic C decreased by 40% (0–10cm depth) and 11–16% (below 10cm) under annual oats and by 16% (0–10cm) under perennial pasture. During 10 days incubation, microbially respired C was lower in soil under annual oats and perennial pasture compared with native pasture. The significant decreases in many of the soil organic C pools in native alpine pasturelands caused by current land uses and associated management raise concerns about their long-term sustainability, and their adverse influence on the global C balance and soil quality, especially in case of annual pasture involving intensive soil disturbances.