A control system for controlling a linear actuator including magnetic bearings for levitating a robot arm and a pulse motor for linearly driving the arm in a non-contact manner is disclosed, which comprises a displacement detection unit including displacement sensors, first and second calculation units, moving amount detection unit and adding circuit. The displacement detection unit detects displacement values of the arm from a reference posture, the first calculation unit calculates guiding (y), levitation (z), roll (p), pitching (q), and yaw (r) control current values in response to the displacement values and provides guiding, levitation, roll, pitching, and yaw control current signals (, , , , ). The moving amount detecting circuit detects a moving amount (X.sub.0) of the arm from a reference position in response to an operation of the pulse motor, and provides a compensation current value (.DELTA.Iq") proportional to the moving amount, and the adding circuit adds the compensation current value (.DELTA.Iq") to the pitching control current signal (). The second calculation unit, in response to the guiding, levitation, roll and yaw control current signals (, , , ) and the added pitching control current signal (+.DELTA.Iq"), calculates drive current control values to compensate drive current flowing through the magnetic bearings.