The vibration and active control of a flexible rotor system with magnetic bearings is investigated using Hybrid Method (HM) and HD° control theory with consideration of gyroscopic effect. The hybrid method which combines the merits of finite element method (FEM) and generalized ploynomial expansion method (GPEM) is employed to model the flexible rotor system with small order of plant. The mixed sensitivity problem of H∞ control theory is applied to design the control of system vibration with spillover phenomena for the reduced order plant. The H2 control design is also employed for the comparison to the Ha' design. The experimental simulation is used to illustrate the effects of control design. It is shown that the HD' controller design can be very effective to suppress spillover phenomena. In addition, H∞ control design has robustness to the variation of the parameters of the model. The application of hybrid method (HM) together with Ha° control design is highly recommended for the vibration control of flexible rotor system with magnetic bearings.