This paper presents a new semi-active control scheme that can reduce the unbalance responses in a flexible rotor system with multiple masses (i.e., disks) using a magnetorheological fluid based squeeze film damper (MR-SFD). The proposed control scheme is designed to effectively attenuate multiple vibration modes of the rotor system. The control algorithm begins with the determination of the optimal location of the MR squeeze film damper to maximize its control performance over several flexural critical speeds of interest. After identifying the optimal position of the damper based on the structure dynamics modification method, the singular value analysis was performed, with varying rotor speed, to determine the scheduled input current to the MR squeeze film damper at each rotational speed. Using a rotor-bearing model coupled with three disks and a MR-SFD, a series of numerical simulations was performed to evaluate the effectiveness of the control algorithm. In addition to the numerical study, a test rotor system (equivalent to the numerical model) and a prototype MR squeeze film damper were constructed and tested to experimentally evaluate the performance of the prototype with the control and validate the simulation results. The numerical and test results indicate that optimal positioning of the damper alone (without implementing the control) significantly reduced the unbalance responses of the disks near the first critical speed. Activating the controller, the damper further attenuated the unbalanced vibrations of the rotor system at the second critical speed. The results show that, at this critical speed, the peak vibration magnitudes of the disks were attenuated by nearly 70%.