Soil aggregates are the basic units of soil structure, and their composition and carbon (C) stability directly affect soil fertility. As cementing agents, humic substances play an important role in the formation and stability of soil aggregates. Long-term fertilization not only changes the structure of humic acid (HA), but also affects the content and stability of organic C in soil aggregates. In this study, based on a long-term fertilization experiment, the relationship between the molecular structure of HA and the stability of organic C in the aggregates was examined. Compared with the non-fertilization control (CK), both the application of organic manure alone (M) and organic manure combined with inorganic fertilizer application (MNPK) increased organic C content in the bulk soil and in HA. In addition, the application of organic manure (M, MNPK) favored the formation of macroaggregates (>0.25 mm) and showed a higher organic C contents of soil aggregates with different sizes than the CK. Moreover, the content of aliphatic C, the ratios of aliphatic C/aromatic C and alkyl C/O-alkyl C was increased with the application of organic fertilizer. A significant negative correlation was observed between aromatic C and organic C content of the aggregates with sizes of >2 mm, 2-0.25 mm, and 0.25-0.053 mm (P < 0.05). The findings indicated that organic fertilization treatments (M and MNPK) increased the aliphatic C content of HA, which favored the increase in the organic C content and stability of the aggregates.