The long-term physicochemical responses of aeolian sandy soil aggregates to different crop rotation patterns are poorly understood. Here, we collected soil samples from the 0–20 cm tillage layer of continuous maize crop and alfalfa–corn rotation plots situated on the edge of the Zhangye Oasis, Northwest China. These samples were analyzed to quantify the influence that both cropping patterns have on the structure, carbon content, and nitrogen content of native aeolian sandy soils. When compared with long-term continuous maize cropping, planting using a maize–alfalfa rotation system significantly increased the mass fraction of macro-aggregates with sizes of >2 mm and 0.25–2 mm from 8.74 % to 12.08 % and 19.1 % to 21.21 %, respectively, but decreased the mass fraction of micro-aggregates (0.053–0.25 mm) from 11.57 % to 8.09 %. Further, there was no significant difference in the content of silt and clay particles between each system. The maize–alfalfa rotation increased the stability of aggregates from 0.32 to 0.37, representing an increase of 15.61 %. Soil organic carbon, inorganic carbon, and total nitrogen were mainly enriched in macro-aggregates with sizes of >2 mm, and silt and clay fractions for both cropping patterns. Implementation of a rotation pattern increased organic carbon contents by 27.21 %, 25.62 %, 26.67 %, and 27.58 %, inorganic carbon contents by 14.40 %, 4.53 %, 53.33 %, and 20.95 %, and total nitrogen contents by 14.40 %, 4.53 %, 53.33 %, and 20.95 % in aggregate particle sizes of >2 mm, 0.25–2 mm, 0.053–0.25 mm, and <0.053 mm, respectively, when compared to continuous corn cropping. Total nitrogen content increased by 29.72 %, 7.02 %, 4.17 %, and 50.00 %, respectively, for these particle size ranges. Maize–alfalfa crop rotation can therefore effectively improve soil aggregate composition and aggregate stability, alongside organic carbon content, inorganic carbon content, total nitrogen content, and their storage capacity. This system thus represents a soil cultivation technique that can increase the soil carbon sequestration capacity in the oasis zone of Northwest China.