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A long-term field experiment was established in 1990 to evaluate the impact of mineral fertilizer (N and NPK) and organic material (manure and crop-residues) application on soil aggregation and organic carbon (C) accumulation in an intensively cultivated grey desert soil in northwestern China. The long-term addition of organic materials with balanced inorganic NPK inputs significantly increased the mass proportion of macroaggregates from 10% in the CK treatment to 34% and 24% in the 1.5MNPK and SNPK treatments (the application of inorganic NPK combined with organic sheep manure and the return of crop residues to the field, respectively). In contrast, the addition of inorganic fertilizer (the N and NPK treatments) had no obvious effect in promoting the percentage of macroaggregates. The application of inorganic fertilizer and abandonment (the CK0 treatment) only sustained the soil organic carbon (SOC) content. However, the SOC contents were significantly increased by 197% and 19% in the 1.5MNPK and SNPK treatments, respectively, relative to the CK treatment over a 24-year period. Amending the soils with N and NPK mainly increased the organic C concentrations in the silt + clay fraction. In contrast, the application of manure accelerated the accumulation of organic C in all of the aggregate fractions, particularly by increasing the amount of C in the fine intra-aggregate particulate organic matter (iPOM) fraction rather than the coarse iPOM or the silt + clay subfraction. The organic C concentration in the silt + clay fraction was significantly correlated with the mass proportion of macroaggregates (R-2 = 0.9488, P < 0.01), and with the ratio of macroaggregates to microaggregates (R-2 = 0.9477, P < 0.01). These results indicated that macroaggregates and the silt + clay fraction were more sensitive to fertilization in the grey desert soils. We consider that increases in the organic C concentrations in the silt + clay fraction and shifts in the stored C towards microaggregates may play important roles in soil aggregation and SOC sequestration in grey desert soils. (C) 2016 Elsevier B.V. All rights reserved.