【Objective】Although many studies have reported the effects of long-term fertilizer application on soil organic carbon composition, molecular structure and functional group, few studies revealed the relationships between soil organic carbon, organic carbon composition and organic carbon functional groups under long-term fertilization conditions. Therefore, a field experiment with a maize-cowpea cropping rotation was conducted. The experiment included three treatments, i.e., organic nitrogen (N)fertilizer (OM), inorganic N fertilizer (IF), and the combination of organic and inorganic N fertilizers (IF+OM). The effect of long-term (9 years) N fertilizer applications on organic carbon composition and molecular structure of soil aggregates were studied to reveal the accumulative mechanism of soil organic carbon. 【Method】The soil was divided into 4 components by dry sieving method: >2 mm, 2-0.25 mm, 0.25-0.053 mm, and <0.053 mm, and then the mean weight diameter (MWD) and geometric mean diameter (GMD) were analyzed. The physical isolation method was used to measure free light particulate organic carbon (fPOC), intra-microaggregate particulate organic carbon (iPOC), silt-clay sized fraction organic carbon within microaggregates (iSOC) and free silt-clay sized fraction organic carbon (fSOC), and nuclear magnetic resonance spectroscopy was used to determine the functional group structure of soil organic carbon. 【Result】The results showed that compared with IF treatment and OM treatment, IF+OM treatment significantly enhanced maize and cowpea yields after 9 years of continuous N fertilization. Moreover, compared with IF treatment, OM and IF+OM treatments significantly increased MWD and GMD, and the effect was more obvious under IF+OM treatment. This study shows that fPOC was the main component of the soil organic carbon fraction, ranging from 21.0 to 29.8 g·kg^-1. The combination of organic and inorganic N fertilizers significantly enhanced the contents of soil organic carbon, fPOC and iPOC by 30.0%, 41.9% and 23.5% relative to IF treatment, respectively, but had no significant effect on the contents of iSOC and iSOC. The type of N fertilizer significantly influenced the ratio of alkyl, alkoxyl and aromatic carbon, which in turn significantly influenced alkyl/alkoxyl carbon and aromaticity in the soil. Compared with IF treatment, the combination of organic and inorganic fertilizer N fertilizers significantly increased alkyl carbon contents, but decreased aromatic carbon. Multi-path analysis showed that the alkyl carbon/alkoxy carbon ratio, hydrophobicity, aromaticity, fPOC and iPOC carbon content were closely related to organic carbon content. 【Conclusion】In conclusion, long-term combined application of organic and inorganic N fertilizers results in increases in crop yields, promotes the transformation of soil fine aggregates to large aggregates, increases fPOC and iPOC contents, optimizes the structure of aggregates, enhances soil stability, and thus promotes soil carbon sequestration, increased organic carbon storage, and thus promotes soil carbon sequestration. These results reveal the improvement mechanism of long-term combined application of organic and inorganic N fertilizers on soil organic carbon content, which would provide a theoretical basis for improving cropland soil fertility and structure.