Active magnetic bearings (AMBs) are often used to mitigate vibrations in turbines, compressors, machining spindles, etc. However, rotor-AMBs are inherent open-loop unstable systems, and hence it is an urgent yet challenging task to stabilize rotor-AMBs with external disturbances. A dual-mode predictive flexible rotor controller is developed hereby for a rotor-AMB system with input constraints. The method is afterwards proved to be capable of enlarging the region of attraction, and hence can effectively mitigate more-intensive vibrations excited by external disturbances, which is desirable in real applications. Finally, experiments are conducted on the rotor-AMB system to show the effectiveness of the proposed dual-mode predictive controller.