In the field of the computer numberical control (CNC) machine, permanent magnet synchronous motor spindle (PMSMS) was used more and more widely. In order to ensure its accuracy, the cogging torque should be reduced. Thus, this is to investigate the impact of different number and different installation position of different size of permanent magnet aimed for PMSMS on the cogging torque ripple. Based on description of the producing mechanism and reducing methods of cogging torque, the moving electromagnetic finite element model (FEM) for PMSMS was built up. The cogging torque of different number and different installation position of different size of permanent magnet of the PMSMS was simulated respectively. At last, the data of the simulation was calculated, analyzed and compared by using MATLAB. The results show that the suitable number and the suitable installation position of different size of permanent magnet can reduce PMSMS's cogging torque effectively.