Organic fertilizers are essential for enhancing soil organic carbon (SOC) levels and promoting sustainable agriculture. The mechanisms of carbon sequestration in upland red soils using various organic materials are not well understood. Here, the impact of various organic fertilization strategies on SOC fractions, functional groups, iron oxides, and soil aggregates was investigated to clarify the protective mechanisms underlying SOC preservation. Six fertilization regimes were examined: no fertilization (CK), mineral fertilizer (CF), 60% mineral fertilizer (RF), RF + straw (RFS), RF + pig manure (RFP), and RF + vermicompost (RFV). The results demonstrated that SOC contents significantly increased by 62.5% in RFP and 63.1% in RFV compared to the CF treatment, with particulate organic carbon (POC) being the primary contributor. Scanning electron microscopy and X‐ray photoelectron spectroscopy demonstrated that RFP and RFV treatments induced the formation of denser flock‐like aggregates and increased aromatic C content, respectively. Fourier transform infrared spectroscopy analysis indicated that RFV treatment exhibited the highest abundance of functional groups among all treatments. SOC and POC were highly positively correlated with soil chemical properties, soil aggregates, poorly crystalline iron oxides, and aromatic rings. Structural equation models indicated that pig manure and vermicompost directly promoted POC accumulation, while straw provided physical protection for POC by enhancing aggregate formation. Furthermore, pig manure indirectly facilitated the development of POC and mineral‐associated organic carbon via soil biochemical properties and iron oxides, respectively. Overall, the application of organic fertilizers enhanced the physical protection, mineral immobilization, and recalcitrance (alkyl C, aromatic C) of organic carbon, facilitating C sequestration and stability. This study highlights the importance of organic management in upland red soils for increasing SOC storage and maintaining global C balance.