The theories of heat transfer, thermodynamics and fluid dynamics are employed to develop the coupled heat transfer analytical methods for the heat-pipe-cooled thermal protection structure (HPC TPS), and a three-dimensional numerical method considering the sonic limit of heat pipe is proposed. To verify the calculation correctness, computations are carried out for a typical heat pipe and the results agree well with experimental data. Then, the heat transfer characteristics and limitations of HPC TPS are mainly studied. The studies indicate that the use of heat pipe can reduce the temperature at high heat flux region of structure efficiently. However, there is a frozen startup period before the heat pipe reaching a steady operating state, and the sonic limit will be a restriction on the heat transfer capability. Thus, the effects of frozen startup must be considered for the design of HPC TPS. The simulation model and numerical method proposed in this paper can predict the heat transfer characteristics of HPC TPS quickly and exactly, and the results will provide important references for the design or performance evaluation of HPC TPS.