A new method of high-speed flow control using permanently operating thermally stratified energy deposition is presented. The paper focuses on the analysis of the dependence of the characteristics of a steady supersonic flow and an aerodynamic (AD) body on the temperature values in the layers of a stratified source and the possibility of making the transition from one steady flow mode to another by changing the temperature in the layers. A detailed visualization of the dynamics of the fields of density, pressure, temperature, and local Mach number is presented during the controlled establishment of steady flow modes. Multiple generation of the Richtmyer–Meshkov instability is shown. The sharp peaks accompanying the development of the Richtmyer–Meshkov instabilities were obtained, which remain in the steady flow mode established under the action of a stratified energy source. Basic approaches for controlling the bow shock wave, drag and lift (pitch) forces (at zero angle of attack), and the stability in a steady supersonic flow past an AD body using permanently operating thermally stratified energy source were developed. The possibility of initiating and damping self-sustained flow pulsations as well as the formation of a steady flow with oppositely directed constantly acting lift forces due to temperature changes in the layers of a thermally stratified energy source is shown.