Aerodynamic heating seriously affects the safety of hypersonic vehicles, which is an urgent problem to be solved. In this work, an aerothermal phase change thermal protection system using foam structure arranged inside aircraft skin is put forward. Firstly, considering the characteristics of aircraft skin, the three-dimensional foam structures, with and without skeleton micropores, is reconstructed. Then, the effects of liquid water mass flow rate and micropores in the foam structure on heat and mass transfer in the aerothermal phase change thermal protection system are investigated. Results show that the aircraft skin temperature decreases fast and then slowly to a platform, with an increase in liquid water mass flow rate. The heat transfer in the foam structure also increases fast and then slowly to a platform, with an increase of liquid water mass flow rate, while the pressure drop for the foam structure increases linearly with an increase in liquid water mass flow rate. The comprehensive heat transfer performance of liquid water flowing along micropores is better than that of liquid water flowing without micropores and vertical to the micropores. The discovery of the above phenomenon helps design a good aerothermal phase change thermal protection system.