Abstract: Agricultural management practices affect carbon sequestration in agricultural soils. This study was performed in southern China to investigate the effects of different fertilizations on soil aggregate organic carbon sequestration and distribution over time in yellow-mud paddy. There were four treatments: no fertilizer (CK), application of chemical fertilizer (NPK), combined application of chemical fertilizer and cattle manure (NPKM), and combined application of chemical fertilizer and straw (NPKS). After 36 years of the experiments (1983 to 2020), the soil samples were collected after rice harvest to analyze soil aggregate, organic carbon sequestration, and distribution. The results showed that macro-aggregates (>2 mm) and medium aggregates (0.25−2 mm) were major components of the bulk soil. Compared to CK, NPKM and NPKS significantly increased the proportions of macro-aggregates by 22.0% and 15.5%, respectively, but greatly decreased the proportions of medium aggregates (0.25−2 mm) by 14.3% and 10.2%, respectively (P<0.05). Application of fertilizer resulted in a significant increase in the organic carbon content of the bulk soil, ranging from 16.9% to 43.9%, compared with the CK treatment. The average organic carbon content of the macro-aggregates was 1.3–1.6 times that of the other aggregates. The organic carbon content of macro-aggregates (>2 mm), medium aggregates (0.25−2 mm), and silt and clay (<0.053 mm) was higher under NPKM than under CK. Furthermore, NPKS increased the organic carbon content of macro-aggregates (>2 mm) compared to CK. The macro-aggregate organic carbon content accounted for 44.5%−63.8% of the total soil organic carbon. Compared with CK, NPKM and NPKS treatments significantly enhanced macro-aggregate organic carbon sequestration by 25.0% and 19.3%, respectively; but decreased the organic carbon sequestration of medium aggregates (0.25−2 mm), micro-aggregates (0.053–0.25 mm), and silt and clay (<0.053 mm). For the macro-aggregates, the light fraction of organic carbon (LF-C) and mineral-associated organic matter (mSOC) were the major parts, and the proportions of mSOC accounted for 50.7%−57.7% of the macro-aggregates. Compared with CK, the content of LF-C increased by 20.7%−32.3% in the fertilization treatments, respectively, and the contribution of LF-C to total soil organic carbon was most significantly increased by 8.9% and 9.4% under the NPKM and NPKS treatments (P<0.05), respectively. For the medium aggregates, the organic carbon content of the fine fraction organic carbon was significantly higher under NPKM treatment than under other treatments (P<0.05); other sub-fractions was not affected by the application of fertilizer. The coarse fraction of organic carbon (CF-C) and mSOC were the major components of the organic carbon in medium aggregates. NPKM and NPKS significantly decreased the sequestration of LF-C, CF-C, and mSOC in medium aggregates compared with the NPK and CK treatments (P<0.05). The organic carbon content of the bulk soil was found to be significantly correlated with rice yield and organic input (P<0.01). Both macro-aggregate organic carbon content and LF-C content showed a significant positive correlation with rice yield (P<0.01). They were also significantly positively correlated with the organic carbon input (P<0.01). Overall, the combined application of chemical fertilizer with cattle mature or straw could increase the proportions and content of organic carbon of macro-aggregates, thus promoting the contribution of total soil organic carbon, especially with the application of cattle manure. Additionally, the combined application of chemical fertilizer and straw was beneficial in promoting macro-aggregate LF-C content and the contribution of total soil organic carbon. The organic carbon content and fractions of active carbon in macro-aggregates are closely related to the productivity of yellow-mud paddy soil. The results provide methods for fertilization management of yellow-mud paddy soil in southern China.