To study the thermal design of a scramjet aircraft, we propose a program for conjugate thermal analysis of an X-51A-like aircraft with a regenerative cooling channel. We comprehensively analyze various factors, including thermal aerodynamics, thermal structure, cooling channels, combustion heating, and heat transfer into the interior spaces of the aircraft. Although various studies have been conducted and published separately on each topic, none have considered these components together. In this study, we developed numerical methods for flow and structural thermal analysis and prediction of surface heating between two domains. A method for applying the heat of combustion to the inner surfaces consisting of surfaces of the inlet, combustion chamber, and nozzle is further introduced. Moreover, methods for computing the coolant flow inside the regenerative cooling channels and coolant-structural heat exchange are proposed. Furthermore, the temperature of the interior spaces of the aircraft, which are occupied by payloads, and the heat transfer into the interior are considered. We then performed conjugate thermal analysis of the X-51A-like vehicle under the following flight conditions using the developed program: Mach 6, and altitude = 22.342 km. Using the computational results, the temperature of each component of the aircraft was thoroughly analyzed: outer surfaces of the scramjet, inner surfaces near the combustion chamber, interior spaces, and coolants flowing in the cooling channels. Finally, the necessity of conjugate thermal analysis for the proper design of the thermal protection system, which requires a comprehensive estimation of the thermal environment inside the scramjet, is examined. (c) 2022 Elsevier Masson SAS. All rights reserved.