This study aimed at investigating the effects of agricultural exploitation on desert soil organic C, N and P, and soil aggregation. Four land uses were assessed: (1) 5-year wheat (Triticum aestivum L.)/barley (Hordeum vulgare L.) + 5-year maize (Zea mays L.); (2) 5-year wheat/barley + 5-year alfalfa (Medicago sativa L.); (3) 6-year wheat/barley + 4-year acacia (Robinia pseudoacacia L.) and (4) uncultivated desert soil. The desert soil contained total organic C (TOC) of 3.1, 3.7 and 4.2 g kg−1 and particulate organic C (POC) of 0.6, 0.7 and 0.8 g kg−1 at 0–10, 10–20 and 20–30 cm depths, respectively. The soil TOC concentration was increased by 32–68% under wheat–maize rotation and by 27–136% under wheat–acacia at 0–20 cm depth, and by 48% under wheat–alfalfa only at 0–10 cm depth. This contrasted with an increase in the soil POC concentration by 143–167% at depth 0–20 cm under wheat–maize and by 217%, 550% at depth 0–10 cm under wheat–alfalfa and wheat–acacia, respectively. The desert soil had 13 Mg ha−1 TOC stock and 2 Mg ha−1 POC stock at depth 0–30 cm, whereas crop rotations increased the soil TOC stock by 30–65% and POC stock by 200–350%. Over the 10-year period, the rates of TOC accumulation were 0.6, 0.3, 0.8 Mg ha−1 year−1 and the rates of POC accumulation were 0.4, 0.4 and 0.7 Mg ha−1 year−1 under wheat–maize, wheat–alfalfa and wheat–acacia rotations, respectively. At 0–30 cm depth, total soil N was increased by 61–64% under wheat–maize and wheat–acacia, but total soil P was reduced by 38% under wheat–alfalfa. A significant improvement in clay stability but not in aggregate water-stability was observed in cultivated soils. The results showed a significant increase in soil organic C pool but unimproved macro-aggregation of the desert soil after 10 years of cultivation.