Objective The aims were to clarify the differences in soil structure and soil organic nitrogen (N) components under N application and different cropping patterns (intercropping and rotation), and to explore the effects of N application and cropping patterns on soil structure and N components, in order to provide a scientific basis for optimizing cropping systems and achieving sustainable agricultural production.

Methods Based on a long-term field experiment established in 2013 in the irrigated desert soil area of the Hexi Corridor in Gansu, two N application rates (0 and 300 kg hm⁻²) and three cropping patterns (maize/soybean intercropping; maize-soybean rotation; soybean-maize rotation) were set up. By measuring the distribution of soil water-stable aggregates, soil bulk density, total porosity, total N, and organic N components under rotation and intercropping conditions in 2024, the differences in the above soil indicators between rotation and intercropping conditions were compared and analyzed to clarify the effects of N application and cropping patterns on soil structure, N components, and N storage.

Result N application significantly reduced the proportion of water-stable macroaggregates (> 2 mm) in the maize zone, increased microaggregates (< 0.25 mm), and decreased aggregate stability (MWD, GMD). It also elevated bulk density and reduced total porosity in the soybean zone, with more pronounced effects under intercropping. Intercropping enhanced maize zone total N by 10.56% and N storage by 10.53%, while increasing acid-hydrolyzable N (19.13%) and amino acid N (21.71%). In contrast, N application in rotation significantly improved soybean zone total N and N storage.

Conclusion Intercropping increased soil bulk density compared to rotation. N application show no significant effect on maize zone N pools, whereas intercropping promoted soil N accumulation relative to rotation. However, rotational N application synergistically enhances soybean zone N storage. Overall, intercropping and rotation exhibite complementary advantages in N pool regulation: intercropping facilitated N activation in maize zones, while rotational N application sustainably improved soybean zone N storage. These findings provide differentiated strategies for crop-soil synergy-driven strategies in Northwest China’s irrigated desert soils.