This paper proposed a new modeling technique and control system design of a flexible rotor using active magnetic bearings (AMB) for motion and vibration control. The purpose of the research was to pass through a critical speed and achieve high-speed rotation. To achieve this, it is necessary to control both vibration and motion. Even though reduced order physical model [1] that we used before is available technique in expressing vibration, this technique cannot express motion. Thus we propose an extended reduced order physical model [2] that can simultaneously express motion and vibration. Further, by using the model we apply the design of a new controller that combined proportional integral derivative (PID) with linear quadratic (LQ) control to a flexible rotor. The procedure we propose is verified by simulations as being effective for a flexible rotor.