Chinese soils that had been cropped to continuous wheat-maize rotation for 10 to 13 years in Guangzhou (tropical red soil), Nanjing (subtropical yellow-brown soil), and Henan (temperate meadow soil) were analyzed to evaluate changes in quantity and quality of soil organic carbon (C) under different fertilization treatments compared to reference soils. Addition of farmyard manure and farmyard manure + NPK fertilizer tended to increase amounts of oxidizable C, microbial biomass C and mineralizable C, while NPK fertilizer only increased microbial biomass C and mineralizable C, and decreased oxidizable C. Among different agroecosystems, oxidizable C, microbial biomass C and mineralizable C in Nanjing were much higher than those in Guangzhou and Henan. When characterized by 13C nuclear magnetic resonance, an influence of fertilization treatment was evident, especially on long chain aliphatic C and carboxylic C. Long chain aliphatic C was the dominant component (34–51%) of the soil organic C. Soil oxidizable C, microbial biomass C and mineralizable C were positively related to carbohydrate C and carboxylic C, and negatively related to unoxidizable C and long-chain aliphatic C.