Many balancing devices have been created to reduce machinery vibration especially in a high-speed rotor system which is very sensitive to the rotating mass unbalance. The best solution is that this device can self-perceive vibration changes and then respond these changes in an optimized way according to the different situations, which means it is a self-recovery system. According to this consideration, an electromagnetic driven bi-disc compensator for rotor auto-balancing is proposed here. In this system, rotor unbalance is online identified and calculated, after that the balancing discs will be driven to the best compensating positions, so that the unbalance can be suppressed or eliminated. Long transition time and transient vibration enhancement are terrible roadblocks which limit the industry applications of such auto-balancing system. To solve these deficiencies, a freely rotation bi-disc strategy was established and the solutions of two special cases were also discussed. A rotor auto-balancing test rig was build up. Experiments using the new solution on this rig showed that the electromagnetic compensator could be moved more accurate and effective, by which not only the balancing time was reduced, but also the transient vibration enhancement was avoided.