A numerical study was conducted to investigate the flow and heat transfer characteristics of a supersonic second throat exhaust diffuser for high-altitude simulations. The numerical results were satisfactorily validated by the experimental results. A subscale diffuser using nitrogen was utilized to investigate starting pressure and pressure variation in the diffuser wall. Based on the validated numerical method, the flow and heat transfer characteristics of the diffuser using burnt gas were evaluated by changing operating pressure and geometric shape. During normal diffuser operation without cooling, high-temperature regions of over 3000 K appeared, particularly near the wall and in the diffuser diverging section. After cooling, the flow and pressure distribution characteristics did not differ significantly from those of the adiabatic condition, but the temperature in the subsonic flow section decreased by more than 1000 K. Furthermore, the tendency of the heat flux from the diffuser internal flow to the wall was similar to that of the pressure variations, and it increased with operating pressure. It was confirmed that the heat fluxes of the supersonic and subsonic flows in the diffuser were proportional to the operating pressure to the 0.8 and −1.7 power, respectively. In addition, in the second throat region after separation, the heat flux could be scaled to the Mach number ratio before and after the largest oblique shock wave because the largest shock train affected the heat flux of the diffuser wall.