A coupling method was presented to deal with the heating problems of hypersonic vehicles in rarefied flow. The DSMC (direct simulation Monte Carlo) method was combined with the heat conduction equation by introducing the Newton cooling law. An efficient loose coupling procedure which can calculate the aerodynamic heat and structure heating of vehicle configuration was designed to simulate the temperature distribution of thermal protection systems. After taking the blunted cone as an example to validate the DSMC code, a numerical experiment was conducted to simulate the structure temperature and heat flux distribution characteristics of the X37B orbital vehicle shape in cruise state. The results show that the presented coupling method can simulate the aerodynamic heating process of a hypersonic vehicle in rarefied flow, and can provide technical support for the design of rarefied-flow hypersonic vehicles in terms of thermal protection systems and aerodynamic heating characteristics analysis.