In order to investigate the structural characteristics of turbulent flow over sand waves on a complicated riverbed, a numerical model for simulating flow over three-dimensional sand waves was established using the Fluent software based on the Reynolds-averaged Navier-Stokes(RANS)equations and the k-ω turbulence model. The model was verified using experimental data. The results show that the established model can depict the turbulent characteristics over sand waves well. The three-dimensional properties of the sand waves are important factors influencing the turbulent structure of flow. The shear stress and bed form resistance are much more sensitive to the transversal phase difference φ₂ than to the longitudinal phase difference φ₁. With the increase of φ₂, the sand waves become interlaced, and the shear stress and bed form resistance both decreased.