The NCAR Whole Atmosphere Community Climate Model, with a quasi‐uniform horizontal resolution of ∼25 km and a vertical resolution of 0.1 scale height, produces large vertical shear of horizontal wind with peaks around the mesopause and the tropical and midlatitude tropopause. In these regions, the static stability also reaches peak values and therefore allows large vertical shears before the onset of dynamical instability. The wind shear peaks near the mesopause and the tropopause from the simulation compare well with those identified in observations, including the magnitude, latitudinal dependence, and large shear statistics. By analyzing the probability density functions of the wind shears and their dependence on the zonal scales, it is found that smaller scale processes, likely gravity waves, contribute significantly to the large shears and may play a dominant role in producing the largest shears. Climatological tidal waves have secondary contribution to the large winds and shears, but spectral analysis suggests that they can modulate wind shear perturbations by gravity waves in the mesosphere and lower thermosphere. Implications for tracer transport and mixing in these regions are explored by estimating diffusion coefficients based on the root‐mean‐square winds, shears, and corresponding spatial scales from model results.