In order to minimizing the rotor displacement and the amplifier current mainly caused by the unbalance forces when the flexible rotor passes the first bending critical speed, the optimal controller is presented in this paper. The accurate modeling method for the flexible rotor based on the sine sweeping measurements is investigated. The design of the Kalman estimator and the choice of the variance matrix elements have been described. The optimal state feedback regulator with an integral controller has been used for stabilizing the system and the determination of the weight matrices has been investigated in detail. The influences of the specific elements of the weight matrices on the resonance peak of the flexible rotor when passing the first bending critical speed are analyzed. Finally, the running up test of the flexible rotor is implemented and the result shows the effectiveness of linear quadratic Gaussian (LQG) controller minimizing the rotor displacement and the amplifier current nearby the first bending critical speed. Furthermore, the comparison between the proportional-integral-differential (PID) controller with phase lead compensator and the LQG controller verifies the superiority of LQG controller in reducing the amplifier currents.