In traditional active flutter control, piezoelectric materials are used to increase the stiffness of the aeroelastic structure by providing an active stiffness, and usually the active stiffness matrix is symmetric. That is to say that the active stiffness not only cannot offset the influence of the aerodynamic stiffness which is an asymmetric matrix, but also will affect the natural frequency of the structural system. In other words, by traditional active flutter control method, the flutter bound can just be moved backward but cannot be eliminated. In this investigation, a new active flutter control method which can suppress the flutter effectively and without affecting the natural frequency of the structural system is proposed by exerting active control forces on some discrete points of the structure. In the structural modeling, the Kirchhoff plate theory and supersonic piston theory are applied. From the numerical results, it can be noted that the present control method is effective on the flutter suppression, and the control effects will be better if more active control forces are exerted. After being controlled by the present control method, the natural frequency of the structure remains unchanged.