Soil samples collected from a 17-year old long-term fertilizarion field experiment in Zhejiang Province, China, were analyzed to evaluate effects of the use of chemical fertilizers and amendment of organic manure on distribution of aggregates and aggregate-associated organic carbon in paddy soil. The experiment was designed to have six treatments, including CK (control, no fertilizer applied), NPKRS (NPK fertilizers and rice straw), NPKOM (NPK fertilizers and organic manure), NPK (NPK fertilizers), RS (rice straw alone), and OM (organic manure alone). The wet-sieving method was used for evaluation of physical stability of soil aggregates and their particle-size composition. Fourier transform infrared spectroscopy (FTIR) was employed to characterize inherent chemical composition of soil organic carbon (SOC) at the molecular level in the 2 ~ 0.25 mm and < 0.053 mm aggregates. In comparison with CK, Treatments NPKOM, OM, NPKRS and RS significantly (p < 0.05) increased the proportion of > 2 mm and 2 ~ 0.25 mm water stable aggregates, and mean weight diameter of soil aggregates, thus enhancing the effect of macroaggregates physically protecting SOC. The SOC content of the bulk soil and all aggregate fractions, as well as the contribution of macroaggregate-associated (i.e., > 2 mm and 2 ~ 0.25 mm) SOC to total soil organic C in Treatments NPKOM and NPKRS were significantly higher than that, respectively, in CK. However, no significant difference was observed in accumulation of SOC between CK and Treatments NPK or RS. The 2 ~ 0.25 mm fraction of aggregates contained SOC, accounting for 34.16% ~ 48.6% of the total SOC in the soils in all the treatments, suggesting that 2 ~ 0.25 mm aggregates were the main carriers of SOC in the paddy soil. The FTIR spectra of the 2 ~ 0.25 mm and < 0.053 mm aggregates show that the ratios of aromatic-C to total SOC in Treatments NPKOM, OM, NPKRS and RS were 29.9% ~ 45.2% higher than that in CK, and 22.3% ~ 36.6% higher than that in Treatment NPK. The highest ratio was observed in Treatment NPKOM. The FTIR spectra also indicate that in Treatments NPKOM, OM, NPKRS and RS aliphatic-C groups increased slowly but steadily. The increases in aromatic-C and aliphatic-C were attributed mainly to the inputs of recalcitrant compounds derived from organic amendments, and/or to the reduction of H-bonded O-H hydroxyl groups of phenols induced by biochemical processes in soils treated with organic amendments. The findings of the research indicate that both enhanced physical protection of SOC by macroaggregates and increased proportion of chemically recalcitrant organic compounds contribute to carbon accumulation in the paddy soil treated with organic amendments, with the most prominent effect being observed in Treatment NPKOM. Long-term combined application of organic manure and chemical fertilizers appears to be a sustainable environment-friendly strategy to achieve both high agricultural production and soil carbon accumulation.