Thermal protecti.on system (TPS) is one of the most important subsystems of hypersonic vehicles which are subjected to severe aerodynamic heating. The reliability and structural integrity of TPS are crucial to the structural safety and integrity of hypersonic aircrafts. During the design and service stages of the TPS, there are numerous inevitable uncertainties in aerothermal environment, material properties, manufacture and assembly errors, analysis modeling errors, et cetera, which have great impact on the reliability assessment of the TPS. In this chapter, the probabilistic heat transfer for TPS is presented to achieve light-weight TPS with high reliability. The uncertainties and their modeling and sampling methods are introduced at first. Then the finite element model and the precise integration method for transient probabilistic heat transfer of TPS are given. Based on the theoretical and numerical methods, the probabilistic design and reliability assessment procedure for TPS are finally formed. A typical multilayer ceramic composite material TPS is used as example to show the effectiveness of the proposed method.