Abstract: 【Objectives】 The study investigated the effects of long-term organic fertilization on the functional genes of soil carbon cycle in southern red soil areas, and provided theoretical reference for the efficient use of soil carbon pool and fertilization strategy in southern rice fields.【Method】 Relying on the long-term positioning experimental platform of Jiangxi Red Soil Research Institute, four treatments were set:no fertilizer treatment(CK), single chemical fertilizer treatment(NPK), early rice green manure Astragalus sinicus L.treatment(M1), and early rice green manure A. sinicus+late rice straw return treatment(M2). Soil samples were collected after the harvest of late rice to determine the basic physical and chemical properties of soil. Real-time fluorescence quantitative PCR technique was used to determine the absolute quantification of soil carbon cycle functional genes, relationship between different active carbon contents and carbon cyclerelated genes and environmental factors was analyzed.【Result】 The results showed that the long-term organic fertilization treatment increased the content of reactive organic carbon in soil organic carbon fractions, of which the contents of easily oxidized organic carbon, hot water extracted organic carbon and soluble organic carbon were significantly higher in M2 treatment than in CK treatment(P<0.05, the same below); the microbial carbon content in the M1 treatment was the highest among the treatments(193.98 mg/kg). The abundance of functional genes involved in carbon hydrolysis, carbon fixation and methane metabolism was low in both M1 and M2 treatments. Correlation analysis showed that functional genes related to carbon hydrolysis(except amyX, IsoP, lig and naglu), carbon fixation(except mcrA) and methane metabolism(except emGDH) were significantly negatively correlated with total potassium, microbial carbon and humic acid/fulvic acid. Carbon fixation and methane metabolism(except emGDH) were positively correlated with pH and available potassium. Random forest analysis showed that long-term organically fertilized paddy soil explained 89.22% of carbon hydrolysis functional genes and environmental factors, 90.12% of carbon fixation functional genes and environmental factors, and 87.14% of methane metabolism functional genes and environmental factors.The structural equation modeling results showed that the mnp and apu genes, mct and rbcL genes, emGDH and pmoA genes directly influenced carbon hydrolysis, carbon fixation and methane metabolism respectively, while soil organic carbon, humin and humic acid/fulvic acid indirectly influenced carbon hydrolysis and carbon fixation gene abundance, and humic acid, soil organic carbon and humin indirectly influenced methane metabolism gene abundance in long-term organically fertilized paddy soils.【Conclusion】 Long-term organic fertilization is conducive to increasing the content of active organic carbon fractions and reducing the abundance of functional genes of the carbon cycle in southern paddy soils. Improving soil stability helps to maintain field productivity in the face of environmental changes.