Abstract: Organic fertilizer application is an essential measure for improving soil organic carbon (SOC) content, promoting soil aggregate formation and improving soil structure. The objectives of this study were to investigate the influences of long-term organic and chemical fertilizer applications on the distribution and stability (in terms of mean weight diameter, MWD) of soil aggregates, aggregate formation in relation to SOC concentration and responses of SOC content of whole soils and different aggregates to cumulative C input. The experiment was initiated in 1986 and included five treatments - no fertilizer (CK), only chemical fertilizer (CF), rice straw plus chemical fertilizer (RS), low manure rate plus chemical fertilizer (M1), and high manure rate plus chemical fertilizer (M2). Soil samples (in the 0-10 cm soil layer) were collected in 2009 to determine aggregate size distribution and SOC content in bulk soil and different aggregate fractions - they are, large macro-aggregates (LM, >2 mm), small macro-aggregates (SM, 0.25-2 mm), micro-aggregates (MA, 0.25-0.053 mm) and silt plus clay (S&C, <0.053 mm) fractions. The ratios and SOC content of particulate organic matter (POM), micro-aggregates (MA-SM) and silt plus clay (S&C-SM) fractions within SM fraction were also analyzed. Compared with CK and CF treatments, combined application of rice straw or manure with chemical fertilizer significantly improved the proportions of LM and SM, and also MWD of the soil aggregates, but reduced S&C content. Changes were more evident in manure treatments (M1 and M2) than in RS treatment, but no significant difference was noted between M1 and M2. Sole chemical fertilization reduced the stability of soil aggregates. In term of SOC concentration within aggregate fractions, it was highest in LM and SM fractions, followed by S&C and then lowest in MA fraction. SOC concentration of aggregates did not increase linearly with aggregates size. Comparing the four aggregate sizes, SM fraction contributed the most to SOC sequestration in bulk soils. Within SM, MA fraction formed the key site for SOC storage. SOC contents of bulk soils, LM, SM and fractions within SM (i.e., POM, MA-SM and S&C-SM) responded positively to cumulative C input, but no apparent changes in SOC were noted for MA and S&C fractions, indicating C saturation in the two fractions. It was concluded that organic amendment (of either rice-residue or manure) promoted the formation of macro-aggregates and improved aggregate stability. However, soil organic matter was not likely the major binding agent driving soil aggregation in red paddy soils.