Soil samples were collected from a long-term field experiment which had four treatments, i.e. compost (CM), half N in compost plus half N in fertilizer (HCM), fertilizer (NPK) and control without any fertilizer or compost(CK) and sifted into macroaggregate (2 000~250 μm), microaggregate (250~53 μm) and silt+clay fraction (<53 μm) suing the wet-sieving method for analysis of molecular structure of the organic matter in the soil and the aggregates on the solid-state ¹³C -nuclear magnetic resonance (¹³C -NMR) spectroscope. It was found that the ratio of alkyl-C/O-alkyl-C increased with decreasing aggregate size, and was also significantly negatively correlated with the C/N ratio（R² = 0.421，p = 0.022）. These findings suggest that the finer the aggregates, the more the organic matter therein decomposed. Compared with CK, treatments HCM and CM increased the ratio of O-alkyl-C or carbonyl-C to total organic C in soil. The increase in the proportion of O-alkyl-C in the soil was mainly attributed to the increase in relative content of methoxyl-C and N-alkyl-C in macroaggregates, and accumulation of carbonyl-C in macroaggregates and microaggregates of the soil. The application of chemical fertilizer increased the ratio of O-alkyl-C and alkyl-C to organic C in the soil. The increase in the proportion of O-alkyl-C was mainly attributed to the increase in methoxyl-C or N-alkyl-C in macroaggregates and O-alkyl-C in microaggregates, whereas that of alkyl-C was mainly observed in macroaggergates. Compared with CK, application of either organic matter or chemical fertilizer reduced the relative content of aryl-C in the soil by 1.8%~4.6%, which was mainly attributed to the decrease in the proportion of aryl-C in macroaggregates and microaggregates; however, in the fraction in the silt+clay the proportion of aryl-C and phenolic-C increased, but that of alkyl-C decreased by 5.9%~7.1%, indicating that fertilization facilitates accumulation of aromatic-C, but weakens that of alkyl-C in fractions small in particle size. All the findings indicate that long-term application of organic manure helps conserve physically the large amount of carbohydrates and organic acids manure carries in in macroaggregates and microaggregates, thus raising the content of organic carbon in soil.