Considering the potentials of Functionally Graded Panels (FGPs) in aerospace field, it is necessary to study the aerothermoelastic behaviors of FGPs in supersonic flows. In this study, Piston Theory Aerodynamics (PTA) and Eckert reference enthalpy method are used to model aerodynamic force and heating, respectively. The 2-D heat conduction equation is solved and the impact of elevated temperature on the mechanical properties of FGPs is considered to build an aerothermoelastic two-way coupling model of FGPs, and Finite Element Method (FEM) is used to approach the solution. As the results, it is found that there exist three different regions in the bifurcation diagram, namely, thermal buckling region, critical region and flutter region. Due to the inhomogeneous distribution of thermal expansion coefficient, the panel buckles up first and then buckles down via vibration, as thermal buckling happens. Also, irregular vibrations are observed in the critical region of bifurcation diagram. In the flutter region, the dynamic behavior of FGPs is discontinuous and very sensitive to initial conditions. With the impact of aerothermoelastic two-way coupling, different FGPs behaviors lead to the differences in temperature distribution. In particular, the final buckling position and vibration center move to lower positions, and lower temperature region near leading edge is left in the FGPs, because of thermal moment. Also, regular vibrations, rather than irregular vibrations, are easy to extract more principal and regular POD (Proper Orthogonal Decomposition) modes. The results presented could be applied to the analysis and design of Functionally Graded Panels in supersonic flows.