A long-term experiment beginning in 1981 in Jinxian County of Jiangxi Province, subtropical China, was conducted in a paddy field under a double rice cropping system with four different fertilization regimes, including 1) no fertilizer as control (CK), 2) balanced chemical N, P, and K fertilizers (NPK), 3) organic manure using milk vetch and pig manure in the early and late rice growing season, respectively (OM), and 4) balanced chemical fertilizers combined with organic manure (NPKM). Samples (0-17 cm) of the paddy field soil, which was derived from Quaternary red clay, were collected after the late rice harvest in November 2003 for determination of total organic carbon (TOC) and total nitrogen (TN) and fractions of organic C and N. Results showed that TOC and TN in the NPKM and OM treatments were significantly higher than those in other two treatments (CK and NPK). Application of organic manure with or without chemical fertilizers significantly increased the contents of all fractions of organic C and N, whereas chemical fertilizer application only increased the contents of occluded particulate organic C (oPOC) and amino acid N. In addition, application of organic manure significantly enhanced the proportions of free particulate organic carbon (fPOC) and oPOC in total C, and those of amino sugar N and amino acid N (P < 0.01) in total N. In contrast, chemical fertilizer application only increased the proportions of oPOC and amino acid N (P < 0.05). There were no significant differences in either contents or proportions of soil organic C and organic N fractions between the NPKM and OM treatments. These indicated that organic manure application with or without chemical fertilizers played the most significant role in enhancing soil organic C and N quantity and quality in the paddy field studied. A long-term experiment beginning in 1981 in Jinxian County of Jiangxi Province, subtropical China, was conducted in a paddy field under a double rice cropping system with four different fertilization regimes, including 1) no fertilizer as control (CK), 2) balanced chemical N, P, and K fertilizers (NPK), 3) organic manure using milk vetch and pig manure in the early and late rice growing season, respectively (OM), and 4) balanced chemical fertilizers combined with organic manure (NPKM). Samples (0-17 cm) of the paddy field soil, which was derived from Quaternary red clay, were collected after the late rice harvest in November 2003 for determination of total organic carbon (TOC) and total nitrogen (TN) and fractions of organic C and N. Results showed that TOC and TN in the NPKM and OM treatments were significantly higher than those in the other two treatments (CK and NPK). Application of organic manure with or without chemical fertilizers significantly increased the contents of all fractions of organic C and N, while chemical fertilizer application only increased the proportions of occluded particulate organic C (oPOC) and amino acid N. In addition, application of organic manure significantly enhanced proportions of free particulate organic carbon (fPOC) and oPOC in total C, and those of amino sugar N and amino acid N (P <0.01) in total N. In contrast, chemical fertilizer application only increased proportions of oPOC and amino acid N (P <0.05). There were no significant differences in either contents or proportions of soil organic C and organic N fractions between the NPKM and OM treatments. These instructions that organic manure application with or without chemical fertilizers played the most significant role in enhancing soil organic C and N quantity and quality in the paddy field studied.