Long-term fertilization has a significant impact on soil organic carbon (SOC) stock. However, fertilization impact on physical fractions of SOC is still poorly understood on sloping upland of purple soil in the central Sichuan Basin, southwestern China. Therefore, this study assessed the impact of long-term different fertilization on soil aggregates distribution and its organic carbon factions under an intensive wheat (Triticum Aestivium L.)-maize (Zea mays L.) cropping system through four fertilization treatments, no fertilizer (CK), applied mineral fertilizer (NPK), pig manure matched with mineral fertilizer (OMNPK), and crop straw residue matched with mineral fertilizer (RSDNPK). Soil samples from 0～20 cm soil layer were separated into four soil aggregations (>2 mm large macroaggregates-LM, 0.25～2 mm small macroaggregates-SM, <0.25 mm microaggregates-M and <0.053 mm slit-clay microaggregates-SC) by using wet sieving method. LM and SM were further separated into particulate organic matter (POM), microaggregates (mM) and the silt-plus-clay fraction (SC). The results showed that the mass percent, organic carbon content and contribution of LM and SM under organic amendments combined with mineral fertilizer (OMNPK and RSDNPK) were significantly increased compared with NPK treatment, indicating that SOC was enriching towards larger soil aggregates under long-term application of organic fertilizer. Furthermore, organic carbon content and storage of POM, mM and SC in large aggregates were significantly enhanced by OMNPK and RSDNPK treatment. In comparison with NPK treatment, OMNPK and RSDNPK treatments significantly increased contributions of POM while decreased contribution of SC in large soil aggregates. The results also showed that it was greatly helpful to enhance POM sequestration and accumulation in large aggregates by long-term application of organic fertilizer. Additionally, the soil organic carbon storage in the whole soil and larger aggregates were dominated by SC fraction, which was helpful to enhance organic carbon sequestration, especially for crop straw return practice on sloping upland of purple soil.