With the adaptation of the FLASH code we simulate magnetohydrodynamic-gravity waves and vortices as well as their response in the magnetized three-dimensional (3D) solar atmosphere at different heights to understand the localized energy transport processes. In the solar atmosphere strongly structured by gravitational and magnetic forces, we launch a localized velocity pulse (in horizontal and vertical components) within a bottom layer of 3D solar atmosphere modeled by initial VAL-IIIC conditions, which triggers waves and vortices. The rotation direction of vortices depends on the orientation of an initial perturbation. The vertical driver generates magnetoacousticgravity waves which result in oscillations of the transition region, and it leads to the eddies with their symmetry axis oriented vertically. The horizontal pulse excites all magnetohydrodynamic-gravity waves and horizontally oriented eddies. These waves propagate upwards, penetrate the transition region, and enter the solar corona. In the high-beta plasma regions the magnetic field lines move with the plasma and the temporal evolution show that they swirl with eddies. We estimate the energy fluxes carried out by the waves in the magnetized solar atmosphere and conclude that such wave dynamics and vortices may be significant in transporting the energy to sufficiently balance the energy losses in the localized corona. Moreover, the structure of the transition region highly affects such energy transports, and causes the channeling of the propagating waves into the inner corona.