This study focused on the development of the unsteady impact of a thermally stratified energy source on a supersonic flow around an aerodynamic (AD) body in a viscous heat-conducting gas (air). Research was based on the Navier-Stokes equations. The freestream Mach number was 2. A new multi-vortex mechanism of the impact of a time-limited stratified energy source on the aerodynamic characteristics of a body was described. Almost complete destruction of the bow shock wave in the density field, due to the multiple generation of Richtmyer-Meshkov instabilities in the region of a stratified energy source, was obtained. The dependences of the dynamics of frontal drag and lift forces of a streamlined body on temperature in the source layers were studied. It was determined that, by changing the temperature in the layers of a stratified energy source, it was possible to obtain more intense vortices accompanying the Richtmyer-Meshkov instabilities, causing a temporary decrease in the drag force of an AD body and ensuring the emergence and unsteady change in the magnitude of the lift (pitch) forces. The main principles of unsteady flow control using a stratified energy source were established.