A high-resolution three-dimensional numerical model is used for studying nonlinear acoustic-gravity waves (AGWs), propagating from the Earth's surface into the upper atmosphere. Wave sources contain the superposition of two AGW harmonics with different periods, wavelengths and phase speeds. Large-scale AGWs change background conditions for the propagation of smaller-scale wave modes and can modulate their amplitudes. Simulations showed that nonlinear interactions might create small-scale structures in the upper atmosphere. Largest amplitudes of temperature disturbances occur at altitudes 100 – 200 km, producing convective instabilities at altitudes 100 – 120 km. Largest wave-induced increases in the mean temperature exist at altitudes 100 – 150 km. Above 200 km, changes in the mean temperature are mainly negative for the smaller-scale wave mode and are positive for the larger-scale mode and for their superposition. Interactions of two waves propagating in opposite directions produce the mean flows directed opposite and along the x-axis at different altitudes. Simulated wave-induced changes in the mean temperature and horizontal velocities produced by wave sources composed of two wave modes in the nonlinear model are different from the sums of respective changes created by the individual modes. These differences show that nonlinear interactions may significantly influence dynamical and thermal effects produced by sets of AGW spectral modes propagating in the atmosphere.