Nutrient additions can increase carbon (C) inputs to soil, but there is no consensus about the response of soil organic C (SOC) storage and C sequestration. For the Tibetan alpine meadows, little is known about the effects and mechanisms of nitrogen (N) and phosphorus (P) addition on SOC stocks. In this study, we applied N and/or P fertilization for 7 years and analyzed soil changes in bulk density, pH, SOC, soil inorganic C (SIC), δ13C, and microbial biomass C (MBC), as well as stocks of SOC, SIC, and MBC for soil to a depth of 40 cm. We found that C:N decreased in 0–20 cm, and pH decreased at both 0–20 cm and 20–40 cm after fertilization. Fertilization with N and/or P decreased SOC stocks in 0–20 cm by 5–12% and SOC stocks from 0 to 40 cm by 3–5%. This SOC stock decline was associated with changes in SOC concentration but not with changes in bulk density. The SIC stock was 18% of total soil C, and was not influenced by either N or P fertilization. Soil δ13C in the 0–20 cm layer was depleted by fertilization with N or N + P, whereas P enriched soil δ13C. Soil MBC was positively correlated with SOC concentration, whereas soil δ13C was negatively correlated with SOC concentration. Soil δ13C, as a proxy of decomposition rate, indicated potentially higher SOC decomposition under N fertilization. These findings suggest that fertilization with N and/or P lowered SOC sequestration in Tibetan alpine meadows.