This paper presents a new modeling method and a control system design procedure for a flexible rotor with many elastic modes by using active magnetic bearings. The purpose of our research is to rotate the rotor for passing through critical speeds caused by flexible modes. To achieve this, it is necessary to control motion and vibration of the flexible rotor simultaneously. The new modeling method named as Extended Reduced Order Physical Model is presented to express its motion and vibration uniformly. By using this model, a PID controller to levitate the rotor and a LQ controller to suppress its vibration are designed.