A field study was conducted at Hetian, southern Xinjiang, northwest China, to investigate root morphology as affected by interspecific interactions between jujube (Ziziphus jujuba Mill.) and wheat (Triticum aestivum L.). The treatments comprised (1) sole wheat, (2) 3-, 5- and 7-year-old sole jujube trees, and (3) intercropping of wheat/3-, 5- and 7-year-old jujube trees. Roots were sampled by auger in each plot down to 100 cm depth at 20 cm intervals in the soil profile and horizontally up to 150 cm away from the base of the trees at 30 cm intervals. All jujube/wheat intercropping systems had advantages of intercropping with a land equivalent ratio (LER) >1. There were significant differences in the contours of both root length density (RLD) and root diameter (RD) in intercropped wheat and jujube in the vertical and horizontal direction at corresponding soil depths but the RLD and RD of the 7-year-old jujube/wheat intercropping system were less influenced by intercropping in this respect than 3- and 5-year-old jujube intercropped with wheat. The roots of both intercropped wheat and jujube had smaller RLD, RD and larger specific root lengths (SRLs) at corresponding soil depths than did sole wheat and jujube. The older the jujube the larger were the SRL values of intercropped wheat and the smaller the RLD and RD of intercropped wheat. The greater the distance from the jujube the less influence there was on the RLD, SRL and RD of intercropped wheat and jujube and the greater the distance from the jujube the smaller was the SRL of intercropped wheat and the greater the RLD and RD of intercropped wheat (but still less than the monoculture wheat). The older the jujube the more developed were the jujube roots so that the smaller the SRL of jujube the bigger the RLD and RD of jujube. Jujube tree roots showed a mainly downward trend and extended laterally 150 cm from the trees resulting in the roots of the jujube trees and the wheat having niche overlap at a soil depth of 20–40 cm. The mechanisms underlying the thinner roots of wheat and jujube require further investigation.