Mathematic model of Active Magnetic Bearing (AMB) flexible rotor system is built. Supporting characteristic of AMB, unbalance response of the system with different control parameters and stability of the system with variable control parameters in rotating state are analyzed, and varying parameter control strategy based on rotation speed is put forward. The experimental setup is established. The signal of the rotation speed is introduced into the digital controller, different control parameters are adopted in different rotation speed section, and dynamic characteristics of the system with varying parameter control strategy is investigated. Theoretical analysis and experimental results show that the varying parameter control strategy can meet requirements of low-frequency and high-frequency dynamic characteristics of the system synchronously, restrain vibration of the rotor effectively, and contribute to safe operation of the system.