A 30a experiment was altered and rice straw (C₃ crop) applied as organic fertilizer was replaced by maize straw (C₄ crop) in 2012. Soil aggregation, aggregate-associated organic carbon contents and its δ¹³C values were measured to determine the effects of following-up fertilization reforming on their distribution and turnover after 3 years fertilization alteration under seven different fertilization treatments, i.e. 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), high organic fertilization treatment changed from original normal organic fertilization treatment (N-H). The results showed that the macroaggregates (>0.25mm) were the dominant component in the red paddy soil under all fertilization treatments, accounting for approximately 72.48%-86.33% of the total soil aggregates. Compared with chemical fertilizer for 30 years, long term application of organic fertilizer(HOM and NOM)significantly increased the ratio of the large macroaggregates (>2mm) and improved MWD. The contents of organic carbon in soil aggregates increased with the increasing particle size of the aggregates, and macroaggregates were more favorable for Soil organic carbon enrichment. Large macroaggregates (>2mm) were the main contributor of Soil organic carbon under organic fertilization treatments (HOM andNOM) in the red paddy soil, while it was small macroaggregates (2~0.25mm) under chemical fertilization treatment. The more application of fresh organic carbon, the higher new soil organic carbon content of whole soil and all sizes of aggregates. The new soil organic carbon was mainly distributed in the macroaggregates (>0.25mm). After 3 years following-up fertilization alteration, the ratio of the large macroaggregates (>2mm), MWD, organic carbon in whole soil, and aggregate-associated organic carbon was improved by 7.08%-73.13%, 5.38%-44.22%, 14.53%-38.50% and 0.70%-35.86% respectively under the treatments of increasing input of organic fertilizer (C-N and N-H), while reduced by 28.17%-43.20%, 21.17%-31.54%, 17.54%-27.30% and 11.49%- 29.77% respectively under the treatments of reducing input of organic fertilizer (H-C and N-C). As a conclusion, the following-up organic fertilization is necessary to maintain or improve red paddy soil aggregation and organic carbon in the southern China.