Physical fractionation technique was used to analyze the content, distribution, and temporal evolution of organic carbon associated with particle-size fractions of grey desert soil under long-term (1990-2007) fertilization. Compared with no fertilization, a combined application of manure and chemical fertilizers increased the organic carbon associated with particle-size fractions significantly, with the highest increment (0.34 g x kg(-1) x a(-1)) in sand. Following also increased the organic carbon associated with clay and silt significantly. Straw return to cropland only maintained the organic carbon content in different particle-size fractions, while long-term application of chemical fertilizers was not beneficial to the organic carbon increase in particle-size fractions. Coarse silt and coarse clay had the highest distribution rates of organic carbon (27.9% and 27.1%, respectively), being the important fractions in sequestrating organic carbon. When manure was applied with chemical fertilizers, the organic carbon in sand was significantly increased by 119.4%, while that in fine silt and coarse clay was significantly decreased by 40.3% and 37.9%, respectively, which resulted in the increase in the ratio of particulate organic carbon content (W(POC)) to mineral-associated organic carbon content (W(MOC)), and improvd soil carbon property. Long-term application of manure combined with chemical fertilizers was the best mode to increase the organic carbon content in particle-size fractions and improve the fertility of grey desert soil.