Background and aims Understanding the relationship between roots, soil moisture, and nutrients in agroforestry systems in irrigated orchards is critical for optimizing orchard management in arid regions. However, there are still many knowledge gaps in this area. Our goals were to (i) explore the spatiotemporal distribution of fine roots for two species under irrigated conditions; (ii) investigate the relationship between fine roots, soil moisture, and nutrients; and (iii) evaluate the productivity of irrigated agroforestry systems.Methods An orchard with soybeans and apples as intercropping materials was established, including single-cropping soybean, single-cropping apple, and apple–soybean intercropping treatments. Data were collected on the spatiotemporal distribution of fine roots and soil resources under apple monocropping and soybean–apple intercropping treatments in 2020–2021, soybean and apple yield, and yield components.Results Compared with apple monocropping, apple–soybean intercropping increased the richness of fine roots in the field. Apple fine roots decreased in the shallow layer and increased in the deep layer in the area where the species overlapped, which increased the soil water content, decreased the nitrate nitrogen content, decreased the effects of soil moisture and nitrate nitrogen on fine roots,increased soybean plant height and leaf area, decreased stem diameter, increased the number of pods per plant and grains per pod, and decreased the 100-grain weight. The LER (land equivalent ratio) = 1.41.Conclusions Irrigated agroforestry increased the richness of fine roots under soybean–apple intercropping, reduced the dependence of root growth on soil resources, eased competition among species, and achieved higher productivity.