Recently developed parameterization of stationary orographic gravity waves (OGWs) generated by the Earth's topography was implemented into a general circulation model of the middle and upper atmosphere. We performed numerical simulations of the zonal mean wind and amplitudes of stationary planetary waves and normal atmospheric modes with periods of 4-16 days at altitudes from the troposphere to the lower thermosphere in January for easterly and westerly phases of the quasi-biennial oscillation (QBO) including and excluding the stationary OGW parameterization. Simulations show that accounting dynamical and thermal effects of stationary OGWs can lead to substantial changes (up to 50-90 %) in the amplitudes of stationary planetary waves. Amplitudes of westward travelling normal atmospheric modes change (up to 50-90 %) at different altitudes and latitudes of the northern hemisphere due to OGW effects. Transitions from the easterly to westerly QBO phases can change planetary wave amplitudes up to ±30-90 % at middle and high latitudes. These changes in PW amplitudes are consistent with distributions of EP-flux and refractive index under different QBO phases simulated including our parameterization of stationary OGWs.