Lime application represents an established approach for ameliorating soil acidity, and understanding its effects on the interactions between aluminum (Al) and iron (Fe) oxides and soil organic carbon (SOC) fractions is essential for promoting sustainable agricultural practices that enhance carbon sequestration. This investigation examined the interactions among Al and Fe oxides and SOC fractions under long-term fertilization and liming. A long-term field experiment was implemented with five treatments: CK (no fertilizer), N (nitrogen fertilizer), NCa (N plus lime), NPK (nitrogen, phosphorus, and potassium fertilizer), and NPKCa (NPK plus lime). Soil samples were obtained from three depths: 0–10, 10–20, and 20–30 cm. The findings revealed that lime application increased SOC by 20.84% under the N treatment but decreased SOC by 9.97% under NPK. At the 0–10 cm depth, dissolved organic carbon (DOC) was substantially higher under NCa (410.51 mg kg^–1) and NPKCa (372.83 mg kg^–1) compared with CK. Particulate organic carbon (POC) and mineral-associated organic carbon (MAOC) demonstrated consistent enhancement under NPK and NPKCa across all soil depths compared with CK. DOC exhibited significant positive correlations with both aluminum (Ald), reactive aluminum (Alo) and aluminum (Alp), indicating a key role of organically bound and reactive Al in carbon dynamics. Compared to the CK treatment, SOC stock increased significantly by 43.49% under NPK and by 36.82% under NPKCa. Structural equation modeling demonstrated that lime application mitigated the negative effects of free Al (Ald) on carbon sequestration, while Fe oxides (Fed) contributed positively to SOC stabilization. DOC showed no significant impact on carbon sequestration rate (CSR), while easily oxidizable carbon (EOC) negatively affected CSR directly. These results highlight the crucial role of lime in improving acidic soil conditions and enhancing the stability and sequestration of soil organic carbon.