A study was conducted to discuss the spatial distribution of root system of jujube trees in jujube-crop intercropping system in Aksu by the layered digging method, in order to provide a theoretical basis for the establishment of root water uptake model for jujube trees, the analysis of ecological characteristics of water, and the determination of application area. Results showed that, in the vertical direction, in the jujube-wheat intercropping system, the jujube roots distributed in the 0-80 cm soil layer, accounting for 82.55% of root biomass and 74.87% of root length density, while in the jujube-cotton intercropping system, the jujube roots distributed in the 0-90 cm soil layer, accounting for 82.66% of root biomass and 66.75% of root length density; in the horizontal direction, in the jujube-wheat intercropping system, the jujube roots distributed in 0-100 cm away from the jujube tree, accounting for 82.10% of root biomass and 56.99% of root length density, while in the jujube-cotton intercropping system, the jujube roots distributed in 0-150 cm away from the jujube tree, accounting for 81.46% of root biomass and 83.80% of root length density. The distribution regularity of root length density of different root diameter classes and total root length density was consistent. Roots of 0- to 1.0-mm root diameter class mainly distributed in the 0-80 cm soil layer and 0-150 cm away from the jujube tree, and the root length density decreased with increasing soil depth and distance from the tree (horizontal direction). Regression equations explaining the relationships between total root length density or total root biomass and the horizontal distance from the tree and soil depth were established.