The rapid development of hyper-sonic vehicles has made the aerodynamic heating problem to be increasingly prominent, and the multi-layer insulation structure is one of the most used methods in the current thermal protection system. However, in the specific design process, some drawbacks, such as the complex multi-layer structural modelling method, the low simulation efficiency and the repeated modelling severely, limit the iterative efficiency. In this paper, a method using offsetting shell elements was proposed to calculate the heat transfer and thermal-mechanical coupling of multi-layer structure, and the reliability of the simulation method was verified by the arc-heater wind tunnel experiments and thermal-mechanical tests with Pearson correlation coefficients more than 0.98. Taking the stiffened structural airfoils as an example, the insulation effects of the different thickness coatings could be quickly iterated using the proposed method, avoiding the problems of repetitive modelling and poor grid quality. Also, the thermal protection risk was identified accurately with the thermal-mechanical coupling analysis.