Abstract: Certain secondary launch vehicle has complex spatial layouts of the auxiliary power system engine, which cause a harsher thermal environment where a large number of components are at the bottom of the rocket body. To address the aforementioned situation, research on the thermal environment at the bottom of the rocket body during the operation of the high-altitude secondary launch vehicle's auxiliary power system is conducted by means of a combined approach which are method of numerical simulation and of wind tunnel testing for validation. Based on the Navier-Stokes component transport equation, the DOM thermal radiation model, and the RNG k-ε model, a gas jet model of a two-stage launch vehicle with complex bottom components at high altitudes has been established. The calculation results indicate that in the operation of the auxiliary power system, the high heat flux regions of the second-stage launch vehicle are mainly concentrated in the short shell behind the fuel tank and the auxiliary power system support. The peak heat flux at the support during the operation of the submerged engine is 300%-400% higher than that of the other components. When the 60 N and 300 N engines operate in the same direction, the heat flux of the other bottom components reaches its peak, with an increase of 300%-600% compared to the other operating conditions. With increasing flight altitude and velocity, the heat flow of each bottom component shows a decreasing trend but with a small magnitude. The calculation results provide important engineering guidance for the thermal protection design of the bottom of the second-stage launch vehicle.