This paper investigates the stability issues of functionally graded material (FGM) panels subjected simultaneously to both aerodynamic and thermal loads. Finite Element Method is employed to model the panel structures and the supersonic aerodynamics is calculated by the first-order piston theory. The critical buckling temperature elevation of the panels is at first predicted. The nonlinear static analysis of the panels is then implemented at certain interval of temperature elevation before buckling onset to obtain structural stiffness matrix. The flutter speed of the panels with updated stiffness matrix corresponding to a certain temperature elevation is estimated. The results show that the FGM panels can offer beneficial effects, especially prevention from buckling. However, if FGM panels integrated with TPS are to be applied on supersonic vehicles, one should pay more attention to the boundary conditions to guarantee the dynamic stability.