The observed seasonal variation of zonal wind reversal in the mesosphere and lower thermosphere (MLT) is often not well captured in whole atmosphere general circulation models (GCMs) with current gravity wave parameterization schemes. In this study, we investigate the possible physical mechanisms controlling this seasonal variation. It is found that adaptation of an anisotropic parameterized gravity wave source spectrum with stronger eastward and weaker westward propagating waves can reproduce this seasonal feature. Furthermore, additional stratospheric forcing is needed to control the large winter stratospheric zonal wind and alleviate the “cold-pole” problem in the southern winter. This is accomplished by the application of an inertial gravity wave parameterization scheme. With these changes, the Whole Atmosphere Community Climate Model with thermosphere and ionosphere extension (WACCM-X) can produce zonal mean zonal wind that is in better agreement with climatology from the stratosphere to MLT, including the seasonal variation of the zonal wind reversal.