One major problem in the development of hypersonic vehicles is severe aerodynamic heating; thus, the implementation of a thermal protection system is required. A numerical investigation on the reduction of aerodynamic heating using different thermal protection systems is conducted using a novel gas-kinetic BGK scheme. This method adopts a different solution strategy from the conventional computational fluid dynamics technique, and has shown a lot of benefits in the simulation of hypersonic flows. To be specific, it is established based on solving the Boltzmann equation, and the obtained gas distribution function is used to reconstruct the macroscopic solution of the flow field. Within the finite volume framework, the present BGK scheme is specially designed for the evaluation of numerical fluxes across the cell interface. Two typical thermal protection systems are investigated by using spikes and opposing jets, separately. Both their effectiveness and mechanisms to protect the body surface from heating are analyzed. The predicted distributions of pressure and heat flux, and the unique flow characteristics brought by spikes of different shapes or opposing jets of different total pressure ratios all verify the reliability and accuracy of the BGK scheme in the thermal protection system analysis.