This paper presents a procedure of calculating cogging torque of Permanent Magnet Synchronous Motor (PMSM) for NC machine tool servo-system based on finite element method (FEM). Simulation models of PMSM are established to complete coupled calculation between magnetic fields and mechanical dynamics. Furthermore, the distributions of magnetic flux and electromagnetic force densities are also gained. Finally, the cogging torque of the motor in operating process is suppressed by changing slot opening configuration. The references for the optimization design on NC machine tool servo-system are provided by the simulation model.