Particulate organic matter (POM) structures of both bulk soil and size fractions of water-stable aggregates from a typical hydroagric paddy soil from Tai Lake region, Jiangsu Province, and a red earth-derived paddy soil in Jiangxi Province, China under long-term different fertilization trials were studied by CPMAS¹³C-NMR spectroscopy. Little variation was found of the composition of C species with size fractions, with the soil types and with the fertilization treatments as POM in both bulk soil and water-stable aggregates. Both soils were composed basically of O-alkyl-C, Alkyl-C and Aromatic-C, with the former being dominating. However, different fertilization treatments modified the proportion of different carbon species of the POM from the bulk samples as the portion of O-alkyl-C was decreased and that of aromatic-C and phenolic-C increased under both organic fertilization and compound fertilization of organic and inorganic fertilizers, indicating the enhanced chemical stability of POM under organic amendments; Whereas, increased portion of O-alkyl-C but decreased portion of alkyl-C, aromatic-C and aromaticity was observed under chemical fertilization only, indicating a more readily decomposable nature. The relative proportion of each C species also differed in water-stable aggregates of the size fractions from both soils and long-term different fertilization treatments, and it modified the interactive effect of POM and water-stable aggregates of the paddy soils, which is less significant for the red earth-derived paddy soil.