With the help of numerical simulation, a detailed analysis of the dynamical effect of the stratospheric quasi-biennial oscillation (QBO) of the equatorial zonal wind on the planetary waves (PWs) up to thermospheric heights is carried out for the first time. The 3-dimensional nonlinear mechanistic model of middle and upper atmosphere (MUAM) is used, which is capable of simulating the general atmospheric circulation from the surface up to 300–400 km altitude. The amplitudes of stationary and westward travelling PWs with periods from 4 to 10 days are calculated based on ensembles of model simulations for conditions corresponding to the easterly and westerly QBO phases. Fluxes of wave activity and refractive indices of the atmosphere are calculated to analyze the detailed behavior of the PWs. The important result to emerge is that the stratospheric QBO causes statistically significant changes in the amplitudes of individual wave components up to 25% in the mesosphere-lower thermosphere and 10% changes above 200 km. This change in wave structures should be especially noticeable in the atmosphere during periods of low solar activity, when the direct contribution of solar activity fluctuations is minimized. Propagating from the troposphere to the upper atmosphere, PWs contribute to the propagation of the QBO signal not only from the equatorial region to extratropical latitudes, but also from the stratosphere to the thermosphere. The need for a detailed analysis of large-scale wave disturbances in the upper atmosphere and their relationship with the underlying layers is due, in particular, to their significant impact on satellite navigation and communication systems, which is caused by amplitude and phase fluctuations of the radio signal.