Abstract: To explore the effect of intercropping on organic carbon sequestration in red soil and its response to phosphorus application, this study was based on a 7-year continuous field experiment in a typical low-phosphorus red soil area of Yunnan, China. Four phosphorus fertilizer gradients — 0 (P0), 60 (P60), 90 (P90), and 120 (P120) kg(P₂O₅)∙hm⁻² were established. The study systematically analyzed the changes in soil organic carbon stock, soil organic carbon fractions, carbon sequestration amount, carbon sequestration rate, soil carbon pool activity index (AI), and carbon pool management index (CPMI), as well as their responses to different phosphorus fertilization levels, under two planting patterns: maize monocropping and maize-soybean intercropping. The results showed that planting pattern and phosphorus application had a significant synergistic promotion effect on the organic carbon sequestration in red soil. Under different phosphorus application gradients, maize-soybean intercropping significantly improved the organic carbon sequestration capacity of red soil. Compared with monocropping, the intercropping increased the SOCs by 21.3%, 31.8%, 30.1%, and 31.1%, and the soil carbon sequestration amount by 42.6%, 49.3%, 42.8%, and 46.1% under P0, P60, P90, and P120, respectively. The highest increases in both indices were observed under P60. Under different phosphorus application gradients, maize-soybean intercropping significantly improved the activity and stability of the red soil carbon pool. Compared with monocropping, intercropping increased the red soil carbon pool AI by 9.0%, 36.1%, 20.3%, and 14.2%; and the CPMI by 25.7%, 86.0%, 54.5%, and 39.7% under P0, P60, P90, and P120, respectively. The highest increases in both indexes were observed under P60. Under different phosphorus application gradients, maize-soybean intercropping significantly increased maize yields. Compared with monocropping, the intercropping increased the maize yield by 38.6%, 46.1%, 24.2%, and 6.5% under P0, P60, P90, and P120, respectively. Regardless of the monocropping or intercropping pattern, rational phosphorus application significantly improved organic carbon sequestration in red soil, with the highest effect observed under P90. The promoting effect of intercropping on red soil carbon sequestration was the highest under P60. In summary, maize-soybean intercropping on low-phosphorus red soil offers significant advantages in promoting soil carbon sequestration and increasing maize yields. The intercropping advantage is optimal at a phosphorus application rate of 60−90 kg(P₂O₅)∙hm⁻². This system is one of the optimized planting modes for increasing maize yields and promoting green, low-carbon development in the red soil region of Southwest China.