[Background] The study was order to investigate the effects of fertilizer application on composition of organic carbon and their relationship with aggregate stability in red soil. [Methods] The composition of soil organic carbon and aggregate stability were determined and analyzed to explore their differences and changing pattern at different soil layers under different treatments (no fertilization as a control , CK; chemical fertilization, NPK; chemical fertilization plus straw, NPKS; pig manure fertilization, AM) in 16 years-fertilizer experiment. [Results] Results showed thatorganic carbon (especially particulate organic carbon ( POC)) in the topsoil (0 - 25 cm) increased under three treatments, as well as the rate of POC/ TOC (total organic carbon); among these three treatments, the effect of AM was the most significant, followed by NPKS and NPK. Compared with CK, TOC, POC and MOC by AM increased respectively in 0 - 5 cm by 120%, 257% and 62%, in 5 - 15 cm by 126%,134% and 79%, in 15 -25 cm by 78%, 228% and 52%. Soil organic carbon was mainly present in the MOC ( mineral-associated organic carbon). Different fertilizer application significantly improved the aggregate stability of surface soil (0 - 15 cm), but the effect of them for the underlying soil was not obvious. Aggregate stability of red soil under different fertilizer application ranked in the order of AM > NPKS > NPK > CK. Compared with CK, mean weight diameter obtained by wet sieving method of AM,NPKS and NPK increased respectively in 0 -5 cm by 44%, 32% and 6%, in 5 -15 cm by 138%, 76% and 46%. Mean weight diameter (MWD) obtained by LB (Le Bissonnais) method at different pretreatment was generally in the sequence of fast wetting (FW) < wet stirring (WS) < slow wetting (SW), and relative slaking index (RSI) was greater than relative mechanical crushing index (RMI) at the same level with all the treatments, indicating that the main breakdown mechanism of the soil aggregates was slaking. Soil aggregate stability was positively correlated with organic carbon. Regression analysis showed that determination coefficient of organic carbon and MWD obtained by wet sieving method, FW and WS of LB method was higher than that of organic carbon and MWD obtained by SW of LB method and the correlation of POC and MWD was the best (R2 = 0.79, 0.80, 0.66, 0.81), indicating that soil organic carbon especially particulate organic carbon content could reduce slaking to enhance aggregate stability, and POC was a good indicator to evaluate the performance of soil aggregate stability indirectly. [Conclusions] These results provide a basis for research of soil structure and soil fertility, and have a valuable reference for soil improvement, soil conservation and sustainable utilization of cultivated land in the Southern Red Zone.