To explore the distribution and mineralization of organic carbon in soil aggregates, this study clarified the effects of long-term application of different organic and inorganic fertilizers on soil organic carbon mineralization and the mechanism of aggregates in this process. This study used the red soil of southern farmland treated with different organic-inorganic fertilizers for 36 consecutive years (1988 to 2023) as the research object. Soil samples were collected at depths of 0-10 cm and 10-20 cm respectively under NPK, NPK+ green manure, and NPK+ barnyard manure treatments. The contents of organic carbon (SOC), the release of CO₂ from soil respiration, soil physicochemical properties and other indicators were determined in the soil and aggregates of different particle sizes. The results showed that under long-term combined application of organic and inorganic fertilizers, in the soil layer of 0-20 cm, (1) compared with the NPK treatment, the combined application of organic and inorganic fertilizers increased the SOC content, with the NPK+ barnyard manure treatment significantly increasing the SOC content by 77.39%. The SOC content of the NPK+ barnyard manure treatment was overall higher than that of the NPK+ green manure treatment. Moreover, organic carbon was mainly distributed in the micro-aggregates with a particle size of less than 0.053 mm in the NPK+ barnyard manure treatment, accounting for 86.43%. (2) The amount of CO₂ and the CO₂/SOC ratio under NPK treatment were significantly higher than those under NPK+ barnyard manure and NPK+ green manure treatments, indicating that the combined application of organic and inorganic fertilizers significantly reduced soil mineralization capacity, weakened respiration, and decreased the release of CO₂. (3) The content of SOC in soil was significantly positively correlated with the contents of TN and TP (P<0.01), and negatively correlated with the contents of CO₂ and fPOC (P<0.05). This indicated that aggregates with a particle size of 0.053-0.25 mm could better protect organic carbon, enhance the physical protective effect and retention capacity for organic carbon, and prevent organic carbon from being decomposed by microorganisms. It could be concluded that long-term fertilization mainly affects the content and distribution of organic matter in aggregates and the mineralization capacity of the soil by influencing the content of nitrogen and phosphorus in the soil. In summary, the combined application of organic and inorganic fertilizers for 36 consecutive years provided a theoretical basis for enhancing and stabilizing soil organic matter in southern farmland red soils and for optimizing the fertilization management model, by increasing SOC content in aggregates, increasing soil nitrogen and phosphorus content, and reducing SOC mineralization.