Soil acidification and carbon sequestration are central challenges for sustainable agriculture, particularly across China’s extensive acidic red soil regions, which comprise 32.4% of the national soil area. This study evaluated the long-term effects of straw and manure incorporation on aluminum (Al) and iron (Fe) oxide fractions, soil organic carbon (SOC) sequestration, and crop yield in acidic red upland soil. A 33-year field experiment was conducted with four treatments: no fertilizer (CK), chemical fertilizer (NPK), NPK plus straw (NPKS), and NPK plus manure (NPKM). Soil samples were collected from three depths (0–10, 10–20, and 20–30 cm), and Al and Fe oxide fractions were quantified. Relationships among Al/Fe fractions, soil pH, and SOC were assessed using ANOVA, Pearson’s correlation, and Redundancy Analysis (RDA). Compared with CK, NPKM increased reactive Al (Alo) by 43.84%, 42.94%, and 43.06% and reactive Fe (Feo) by 132.98%, 91.54%, and 55.75% at 0–10, 10–20, and 20–30 cm, respectively. The highest carbon sequestration rate (0.21 t ha⁻¹ year⁻¹) occurred under NPKM in the 0–10 cm depth. Strong positive relationships were observed between reactive/non-crystalline Al and Fe oxides and both SOC sequestration and crop yield, particularly within the 0–20 cm depth, while SOC stock and CSR declined with depth across all treatments. These results highlight the critical role of manure in alleviating soil acidity, enhancing SOC stabilization capacity, and increasing crop productivity in acidic red upland soils. Overall, integrating organic amendments such as manure and straw substantially improves SOC accumulation and supports sustainable agricultural management in acidic red soils.