A 30-year experiment was altered, and aggregate-associated organic carbon fractions based on density fractionation scheme and its δ13C value were measured to study the changes of following-up fertilization reforming on their content and distribution after 3-year fertilization alteration under 7 fertilization treatments, inculding high organic material (HOM), normal organic material (NOM), chemical fertilizer (CF), normal organic fertilization treatment changed from chemical fertilization treatment (C-N), chemical fertilization treatment changed from original normal organic fertilization treatment(N-C), chemical fertilization treatment changed from original high organic fertilization treatment (H-C), and high organic fertilization treatment changed from original normal organic fertilization treatment (N-H), which were analyzed to provide scientific basis for controls of soil fertility and organic carbon management. The results showed that compared with 30-year application of chemical fertilizer,, long term application of organic fertilizer significantly increased the content of total aggregate-associated organic carbon, coarse free particulate organic carbon (cfPOC), fine free particulate organic carbon (ffPOC), occluded particulate organic carbon (oPOC) and mineral-associated organic carbon (MmMOC). The fPOC with the highest magnitude of increase by 67.5% to 150% indicated that it was more sensitive to the fertilizations than other organic carbon fractions. After 3-year following-up fertilization alteration, total aggregate-associated organic carbon, cfPOC, ffPOC, oPOC and MmMOC were improved by 5.2% to 15.5%, 2.8% to 40.2%, 18.9% to 43.9%, 2.8% to 17.6% and 5.1% to 8.2% under the treatment of increasing input of organic fertilizer (C-N and N-H), respectively, while those under the reducing input of organic fertilizer treatments (H-C and N-C) were reduced by 15.8% to 20.9%, 12.6% to 26.9%, 24.6% to 48.4%, 19.9% to 23.9% and 4.9% to 21.9%. The MmMOC, accounting for 50.4% to 59% of total aggregate-associated organic carbon, was the main form for organic carbon sequestration in red paddy soil under all fertilization, while oPOC accounted for 11.3% to 13.4%. The application of fresh organic carbon resulted in the higher content new soil organic carbon content of macroaggregates and all aggregate-associated organic carbon fractions. About 45.6% to 50.1% of fresh organic carbon was transferred to MmMOC, 34.1% to 42.3% to fPOC and 11.8% to 18% to oPOC. As a conclusion, the following-up organic fertilization is necessary to maintain or improve red paddy soil aggregate-associated organic carbon fractions in the southern China.