An analysis procedure for the combined problem of control algorithm and aeroelastic system which is based on the computational fluid dynamics(CFD) technique has been developed. The aerodynamic forces in the transonic region are calculated from the transonic small disturbance(TSD) theory. An linear quadratic regulator(LQR) controller is designed to suppress the transonic flutter. The optimal control gain is estimated by solving the discrete-time Riccati equation. The system identification technique rebuilds the CFD-based aeroelstic system in order to form an adequate system matrix which involved in the discrete-time Riccati equation. Finally the controller, that is constructed on the basis of system identification technique, is used to suppress the flutter phenomenon of the airfoil with attached store. This approach, that is, the CFD-based aeroservoelasticity design, can be utilized for the development of effective flutter controller design in the transonic region.