<p>Stiffened thin-walled structures (STWS) in scramjet engines are considered to be ideal components for achieving the lightweight of load-bearing structures due to their high specific strength and stiffness. However, the large thermal deformation of STWS under the high thermal load region causes adverse effects on the aerodynamic performance and stability of the vehicle. In this paper, we innovatively propose a regional compliance objective function to customize the topology of the thermoelastic problem in STWS and achieve the integrated height and layout optimization based on the Heaviside function directional growth topology parameterization method for thermoelastic structures to achieve lightweight and conformal design. By avoiding the direct influence of thermal load on the objective function, the gray-scale problem and no-material effect in the case of the large thermal load ratio factor are effectively solved. As a result, compared with the traditional method, the method generates a clear stiffened structure, which reduces the maximum deformation of the isolator by 73.93%. This new topology optimization method provides new insights into STWS design in thermal load-dominated scramjet engines.</p>