Because the magnetic bearing supports levitating body without contact, wear, noise and vibration, it is very useful to high revolution machinery. In this paper we selected ATmega 128, a less expensive and widely used micro controller, for control the magnetic bearing system. And we selected the sampling time and the control gain of PID controller through trial-and-error. The control program of the one board controller utilized lookup table to reduce calculation time, and bit shifting for the integer calculation in instead of floating point calculation. As the results, the controller carried out relatively high speed PID control on sampling time 0.25 ms. At last the rotation test for the magnetic bearing system was carried out by 3 phase induction motor and air turbine.