With the increasing of telescope aperture, the main axis driving motor is becoming larger and larger, and the segmented motor has become a hot topic in international astronomy research today. The current harmonics of the segmented Arc Permanent Magnet Synchronous Motor (APMSM) influence the tracking accuracy of the large aperture telescope. According to the mathematical model and harmonic analysis of segmented APMSM, a current harmonic suppression algorithm based on Quasi-Proportional Resonant (QPR) controller was proposed, and the current controller of unit segmented APMSM was designed. The effect of PI and the QPR controller on current harmonics from simulation and experiment was compared respectively. The experimental results show that when using QPR controller, the 5^th harmonic order, the 7^th harmonic order, the 11^th harmonic order and the 13^th harmonic order of the stator current are reduced by 63.3%, 34.4%, 51% and 59.2%, respectively, and the current harmonics of segmented APMSM can be reduced greatly, the tracking accuracy of the large aperture telescope can be improved.