Context: Intercropping legumes with fruit trees in arid regions offer potential for sustainable intensification, yet interspecific competition often compromises crop yields. Balancing resource partitioning and productivity remains a critical challenge. Objective: This study compared the agronomic performance of apple/soybean intercropping (IAS) and apple/ alfalfa intercropping (IAA) intercropping systems in China's arid zone, focusing on yield trade-offs, root niche segregation, and soil nitrogen dynamics. Methods: Root distribution patterns, soil inorganic nitrogen content, dry matter allocation, and land equivalent ratio (LER) were quantified across monoculture and intercropped systems using root-drill sampling and spatial regression models. Results and conclusion: Intercropping reduced soybean and alfalfa yields by 42-54 % and apple yields by 29.54 %37.99 % compared to monocultures. However, the IAS system achieved higher land-use efficiency (LER: 1.22-1.28) than IAA (1.15-1.19), driven by soybean's adaptive root plasticity under shade. Vertical root stratification (apple roots in the 20-40 cm soil depth vs. crops in the 0-20 cm soil depth) minimized competition, while intercropping increased soil ammonium-N by 55.47-60.09 % and reduced nitrate-N leaching by 22.3-27.5 %. Soybean allocated more biomass to stems under shading, whereas alfalfa prioritized root growth after mowing. Despite yield penalties, the IAS system demonstrated superior systemic productivity through niche complementarity and nitrogen cycling optimization. Significance: These results highlight the importance of species selection and root management in designing sustainable agroforestry systems for arid regions.