Fertilizer application is one of the most important management practices for improving soil fertility and increasing crop yield. However, it is far from certain how different forms of fertilizer affect the soil aggregate composition and carbon and nitrogen dynamics, especially for reddish paddy soils although it is one of the most popular soil types in China. A long-term field experiment has been established on a reddish paddy soil of Qianyanzhou Ecological Experiment Station (114°53'E,26°48'N) in Jiangxi Province in 1998. Four treatments were carried out: Control with no fertilizer (CK), straw return (ST), mineral fertilizers (NPK) and pig manure (OM), aiming to evaluate the effects of different forms of fertilizer on the distribution of soil aggregates and carbon and nitrogen content. The results showed that: (1) under control treatment, the <63μm particles (silt and clay) are the dominant component in the soils, accounting for approximately 41%-54% of bulk soil, followed by 63-250μm microaggregate and 250-500μm macroaggregate. Compared with CK, long term application of NPK and OM significantly increased the fraction of 250-500μm particles and decreased the fraction of <63μm particles, and the application of OM significantly increased the particles of 63-250μm and of 250-500μm; (2) the long-term application of ST, NPK and OM increased the organic carbon and total nitrogen contents in the three aggregates, following the order of CKC (carbon enrichment) and E_N (nitrogen enrichment) were >1 in the aggregates of 63-125 μm and <63μm, suggesting that the <125μm aggregate made dominant contribution to the total organic carbon and nitrogen storage in the reddish paddy soil. This study provides fundamental information for choosing proper fertilization practices to improve soil fertility.