Aeroelastic modelling and stability analysis of wing with morphing trailing edge have attracted more and more attention. In order to explore the methods and characteristics of active flutter suppression of wings with morphing trailing edge compared with conventional control surfaces, this paper provides a comparative study of active flutter suppression when the aircraft wing is equipped with morphing trailing edges and conventional control surfaces. The complete aeroelastic system of a small aspect ratio wing is modeled using finite element analysis, coupled with unsteady aerodynamics based on Doublet–Lattice Method. Morphing trailing edges and conventional control surfaces deflection modes are considered when generating the unsteady aerodynamic forces. The state-space system is generated by applying rational function approximation technique based on Minimum State method, and the active flutter suppression control law is searched by using the Linear–Quadratic–Gaussian method. The numerical study verified the feasibility of the proposed modeling approach. It shows that the closed-loop system with morphing trailing edges increases the critical flutter speed up to 22%, which is higher than with conventional control surfaces, and requires smaller deflection amplitude.