;Recently, research of active magnetic bearings has been widely applied in industry. It’s non-contact characteristic of magnetic levitation technology without physical friction and abrasion. Therefore, active magnetic bearings have been widely implemented, such as engineering industry and biomedical application. For example, turbine engine [1], vacuum pump[2], high-speed spindle[3], and so on. Rotating mechanical umbalance causes severe system vibration. The synchronous vibration caused by eccentricity of the rotor is the major excitation source, when rotating at high speed. As the operating speed increases to certain speed, the centrifugal force makes the bearing vibrate larger than the size of air gap, the rotor and the emergency bearing will collide with each other. This paper aims to develop unbalanced compensation of active magnetic bearings base on a digital processor. First, inductive displacement sensors and PD controller are used to levitate the maglev bearing. A generalized notch filter is used to eliminate the synchronous unbalance operating and implement the auto-balancing control of the active magnetic bearing, when the magnetic bearings are operated to certain speed.