Because the facts that numerical models based on Reynolds averaged Navier-Stokes equations cannot accurately simulate the 3D flow structures of compound open-channel flows and the high computational cost of traditional large eddy simulation (LES) method, a three-dimensional numerical model with wall-modelled large eddy simulation (WMLES) was developed to simulate the flow structure in a compound open-channel flow with a depth ratio of 0. 5 in the present study.The numerical model was verified against the detailed experimental data of Tominaga et al. and the existing results of LES.The results show that the model with WMLES is accurate in the simulation of mean velocities, bed shear stress, turbulence intensities, turbulent energy, Reynolds stresses and secondary currents. The model is reliable in 3D numerical simulations of compound open-channel flows. Comparing to the traditional LES method, the WMLES method is able to significantly reduce the computational cost.