In grassland ecosystems, N and P fertilization often increase plant productivity, but there is no concensus if fertilization affects soil C fractions. We tested effects of N, P and N+P fertilization at 5, 10, 15 g m-2 yr-1 (N5, N10, N15, P5, P10, P15, N5P5, N10P10, and N15P15) compared to unfertilized control on soil C, soil microbial biomass and functional diversity at the 0-20 cm and 20-40 cm depth in an alpine meadow after 5 years of continuous fertilization. Fertilization increased total aboveground biomass of community and grass but decreased legume and forb biomass compared to no fertilization. All fertilization treatments decreased the C:N ratios of legumes and roots compared to control, however fertilization at rates of 5 and 15 g m-2 yr-1 decreased the C:N ratios of the grasses. Compared to the control, soil microbial biomass C increased in N5, N10, P5, and P10 in 0-20 cm, and increased in N10 and P5 while decreased in other treatments in 20-40 cm. Most of the fertilization treatments decreased the respiratory quotient (qCO2) in 0-20 cm but increased qCO2 in 20-40 cm. Fertilization increased soil microbial functional diversity (except N15) but decreased cumulative C mineralization (except in N15 in 0-20 cm and N5 in 20-40 cm). Soil organic C (SOC) decreased in P5 and P15 in 0-20 cm and for most of the fertilization treatments (except N15P15) in 20-40 cm. Overall, these results suggested that soils will not be a C sink (except N15P15). Nitrogen and phosphorus fertilization may lower the SOC pool by altering the plant biomass composition, especially the C:N ratios of different plant functional groups, and modifying C substrate utilization patterns of soil microbial communities. The N+P fertilization at 15 g m-2 yr-1 may be used in increasing plant aboveground biomass and soil C accumulation under these meadows.