The flow fields over a simplified 3D hill covered by vegetation have been examined by many researchers. However, there is scarce research giving the three-dimensional characteristics of the flow fields over a rough 3D hill. In this study, large eddy simulations were performed to examine the coherent turbulence structures of the flow fields over a vegetation-covered 3D hill. The numerical simulations were validated by the comparison with the wind-tunnel experiments. Besides, the flow fields were systematically investigated, including the examinations of the mean velocities and root means square of the fluctuating velocities. The distributions of the parameters are shown in a three-dimensional way, i.e., plotting the parameters on a series of spanwise slices. Some noteworthy three-dimensional features were found, and the mechanisms were further revealed by assessing the turbulence kinetic energy budget and the spectrum energy. Subsequently, the instantaneous flow fields were illustrated, from which the coherent turbulence structures were clearly identified. Ejection-sweep motion was intensified just behind the hill crest, leading to a spanwise rotation. A group of vertical rotations were generated by the shedding of the vortex from the lateral sides of the hill.