Abstract: Recently, the shape imitation experiment of cubes has been widely used as a powerful tool to study the dispersal of urban atmospheric boundary layers. As this techonology progresses, better design of the experimental cubes is required to simulate real urban canopies. A Large-eddy simulation was performed to study the effect of different arrangement and height heterogeneity of cube canopies. The effects of the streamwise structure homogeneity and cube height heterogeneity on the flow in the canopies were also discussed. Results show that the fluid structure is significantly influenced by the streamwise mixedness of inhomogeneous structures. The height heterogeneity of cubes would also change the flow, and the change in the flow varies with the arrangement of cube canopies. The effective transport of momentum by turbulence is related to the cube height heterogeneity in the canopies, and it is smaller in canopies of which cubes are more homogeneous in the streamwise direction.