Abstract: Studies on organic carbon gas exchange and runoff loss in farmland soil are relatively isolated, and the synergy between the two pathways is poorly understood. In this study, simultaneous tests of organic carbon gas exchange and soil–water interface migration process of purple soil under different fertilization treatments were conducted using a runoff plot that allowed interflow observation. The experimental treatments included no fertilizer (CK), chemical fertilizer (nitrogen, phosphorus, and potassium; NPK), pig manure plus synthetic NPK fertilizer (OMNPK), and the incorporation of crop residues plus synthetic NPK fertilizer (RSDNPK). The results showed that 1) the soil respiration rate and carbon dioxide (CO₂) emission flux under different fertilization treatments were RSDNPK > OMNPK > NPK > CK, indicating that the application of chemical fertilizer, organic fertilizer, and straw returning increased the soil respiration rate of purple soil. The CO₂ emission flux of RSDNPK was 4155.87 kg(C)∙hm⁻², significantly higher than those of the other fertilization treatments. 2) The soil organic carbon runoff loss flux was in the order of RSDNPK > OMNPK > CK > NPK, and there were differences in the runoff loss pathways under different fertilization treatments. RSDNPK reduced sediment erosion and significantly increased the flux of dissolved organic carbon (DOC) loss in the interflow, reaching 8.29 kg(C)∙hm⁻². The DOC loss flux of the interflow accounted for 49.82%–92.11% of the total runoff carbon loss flux under different fertilization treatments, indicating that interflow was the main pathway of soil organic carbon loss in purple soil. 3) The total fluxes of soil organic carbon loss under RSDNPK were significantly higher than those under other fertilization treatments, which was not significantly different between OMNPK and NPK. The proportion of CO₂ emission fluxes to the total fluxes was more than 99% in each fertilization treatment, indicating that gaseous loss was the main mechanism of organic carbon loss in purple soil. 4) We calculated the carbon loss flux per unit yield for each fertilization treatment and combined the economic benefits with the ecological environmental load. The results showed that the carbon loss flux per unit yield in CK was significantly higher than that in other fertilization treatments. The soil organic carbon content of the OMNPK treatment was 5.86 g∙kg⁻¹, greater than that of NPK, indicating that organic fertilizer application is beneficial to the accumulation of soil organic carbon. OMNPK should thus be prioritized in the purple soil area.