The flutter behavior of thermoplastic composite structures in high-speed flow is a key problem in the design of reusable spacecraft. Based on the classical Mindlin thick theory, the Von-Karman larger deformation theory and the piston theory, the thermoplastic composite structure panel and its aerodynamics were described, along with the consideration of both the thermal stress and the variation of mechanical properties caused by the temperature. The aeroelastic model of the thermoplastic composite panel was established based on the principle of virtual work and the finite element method,and the V-g method and the Newmark method were used to solve the thermal flutter characteristics of the thermoplastic panel from frequency domain and time domain, respectively. After the validity and convergence of the presented method were verified, the effects of temperature on mode coupling in frequency domain, limit cycle oscillation in time-domain and stress response were investigated.The results show that the flutter dynamic pressure obtained by considering the temperature variation of thermoplastic materials will further reduce the flutter dynamic pressure of the panel, and the equivalent stress of thermoplastic panels under the limit cycle oscillation is lower than the material yield limit.