Corrugated core sandwich structures have great potential in the application to thermal protection system of aerospace vehicles. However, the traditional layout of web plates could inevitably lead to thermal short effects and high risk of buckling failure of the integrated thermal protection system (ITPS). In this paper, a novel double-layer ITPS is proposed by splitting and reorganizing a classical corrugated sandwich structure without additional introducing of weight. Distribution types of parallel, symmetric, and orthogonal of the double layers are designed and studied in detail. Basic theory of the thermomechanical problem as well as finite element simulation is carried out to study the responses of the ITPS. Numerical results show that the orthogonal type has more excellent yield resistance at high temperature and large temperature gradient than the others, while the parallel type has a relatively stronger buckling resistance. In addition, the structural stiffness variation caused by temperature dependencies of material parameters is greater than that caused by thermal stress, which shows the significance of consideration of temperature-dependent material properties in structure vibration analysis.