【Objective】 This study aimed (i) to investigate processes and mechanisms of long-term application of crop straw and pig manure affecting content and fractionation of organic carbon pools in upland red soil; (ii) to analyze effect and adaptability of the RothC model simulating changes in organic carbon in upland red soil; and (iii) to provide reference data for management of organic carbon and sustainable development of agriculture in upland red soil. 【Method】 Soil samples were collected from the topsoil layer (0 ~ 20 cm) of a upland of red soil, where out laid were the four treatments, that is, CK (chemical fertilizer), PS (peanut straw), RS (rice straw) and PM (pig manure), in the National Agro-Ecosystem Observation and Research Station in Yingtan, Jiangxi Province of China. Organic cabon in the soil samples was extracted and sorted into five fractions, i.e. particulate organic carbon (POC), organic carbon in sand and stable aggregates (SAOC), dissolved organic carbon (DOC), labile organic carbon (LOC), and inert organic carbon (rSOC), with the modified Zimmermanns’ method. Based on the RothC model, the above-listed fractions of soil carbon were further sorted separately into five subfractions, i.e. organic carbon in readily-decomposable plant residue (DPM), organic carbon in hardly-decomposable plant residue (RPM), microbial biomass carbon (BIO), organic carbon in humus (HUM) and inert organic carbon (IOM). Content and proportion of each fraction and subfraction was determined for analysis of effects of the long-term fertilization relative to treatment. And relationships of each carbon fraction or subfraction with soil iron-aluminum oxides and input of extraneous carbon were analyzed and discussed. 【Result】 Results show that in terms of content and proportion, the fractions of organic carbon in the upland red soil exhibited an order of SAOC > rSOC > LOC > POC > DOC and HUM > IOM > RPM > BIO > DPM. Compared with CK, Treatment PM was 17.0% , 86.7% and 86.7% higher in SOC, DPM and RPM, respectively, and Treatment PS was 94.4% higher in both DPM and RPM. However, the three fertilized treatments did not have much impact on content and proportion of the fractions of BIO, HUM and IOM. The correlation analysis shows that the fraction of rSOC(IOM) was negatively related to free aluminum oxides in the soil, but positively with amorphous - iron oxides in content; that POC was ultra-significantly and positively related to DPM and RPM; that SAOC was significantly and positively related to BIO and HUM; and that rSOC(IOM) was ultra-significantly and negatively related to LOC. 【Conclusion】 Long-term fertilization significantly increases soil organic carbon in red soil upland, but the effect varies with fertilization practice. However, the increasing trend levels off after 26 years of fertilization, thus, in the RothC model, the effects of amendament of organic manure to chemical fertilization on BIO, HUM and IOM appear to be quite insignificant. In the soils applied with PS, RS or PM, organic carbon is dominated with SAOC (63 ~ 2 000 μm) and rSOC (0.45 μm ~ 63 μm) in HUM and IOM. Long-term chemical fertilization amended with PS or PM brings a large volume of carbon into the soil and significantly increases the proportions of DPM and PRM, while amendament of RS can significantly promote transformation of organic carbon from DPM and PRM into BIO and HUM, thus improving soil quality of the farmlands. Long-term fertilization high in organic carbon input and high soil free - aluminum oxides content both accelerate sequestration of inert organic carbon by soil microorganisms.