The exact contribution of arbor roots to the shear strength of root-soil composites at different soil depths requires further investigation. Taking Malus halliana Koehne as the research object, the root distribution along the soil depth was obtained by the longitudinal profile method. A total of 384 samples of undisturbed root-soil composite were obtained from two profiles (0.5 m profile and 1.0 m profile) by using a self-fabricated ring knife. The large-box direct shear tests were carried out to investigate the depth-dependent variations in shear strength and its parameters (cohesion and internal friction angle) of the undisturbed root-soil composites. The results showed that the shear strength and cohesion of the undisturbed root-soil composite increases first and then decreases with the increase of soil depth, which is consistent with the results of root investigation. The soil shear strength increases by 0.3% ~ 20.7% and the cohesion increases by 4.2% ~ 32.7% with the presence of Malus halliana Koehne roots. The roots play a dominant role in strengthening the shear strength of the undisturbed root-soil composite in the depth range of 0–0.4 m. The shear strength values of the two profiles are intertwined after the comprehensive action of multiple factors in the depth range of 0.4–0.8 m. The soil depth of 0.3–0.4 m with the largest number of roots and the richest species of root diameters shows the optimal shear resistance. The research results have important theoretical insights to reveal the interaction between arbor roots and undisturbed soil under different soil depths.