Active magnetic bearings （AMBs） are ideal bearings for high speed and high power rotating machinery for its adjustable stiffness and damp. In this paper，a dynamic model of AMBs-flexible rotor system is established. Aiming at suppressing vibration displacement of the rotor system in passing through the first bending critical speed region，a control which combines a decentralized PID controller and input second filter in series is designed and the controller performances are simulated. The experiments in simulated rotation and real acceleration operations are carried out in a platform of AMBs-flexible rotor system. The rotor system can smoothly pass through its first bending critical speed region and the maximum rotor vibration displacement in acceleration operation is less than half of backup bearing gap. The rotor vibration displacement and current responses of the rotor in different unbalances are measured in order to analyses the influence of the rotor unbalance on vibration characteristics of AMBs-flexible rotor system. It is shown that the proposed controller can make the rotor system smoothly pass through its first bending critical speed region. The rotor imbalance has a significantly influence on the control performance and stability of AMBs-flexible rotor system. The experiment results give a support on the high-performance control strategy of AMBs-flexible rotor system.