This study conducts a two-dimensional computational analysis on high-speed vehicle inlet and isolator configurations, exploring various heat transfer boundary conditions. Five conditions—adiabatic, constant, axial-constant, conjugate heat transfer with adiabatic condition, and constant condition—are examined. Significant differences in density are observed depending on wall temperature. Examining temperature and velocity profiles at the separation bubble location indicates that as the temperature differential between the wall and fluid widens, the slope of the profiles becomes less steep compared to the temperature boundary layer. These findings indicate that the heat transfer boundary condition of the wall influences the structure of the separation bubble, as well as the interaction and reflection point of the shock wave, and the shock-train inside the isolator.