For the optimization of three-phase hybrid stepper motors with complex electromagnetic structures, an optimization method is presented in this paper. The method is a combination of 3D-FEM and the Taguchi optimization method intended to reduce the dependence on FEM results during the optimization calculation. In this paper, the optimization method is used in the optimization of the tooth shape of the three-phase hybrid stepper motor, and the objective is to reduce the noise caused by harmonics in the "torque-angle characteristic" of the motor. It is clear that traditional optimization methods make it very difficult to carry out such an optimization calculation as a large number of finite element calculations have to be used in the optimization process, and the required computation time is extremely long. Using the optimization method presented in the paper, the optimization becomes feasible because the number of finite element calculations is greatly reduced and the computation time is thus greatly reduced. In order to check the effectiveness of the optimization, the waterfall diagram for noise analysis and its application to check torque ripple are also presented in the paper. Both simulation and test results show that the optimized structure can significantly reduce the motor noise caused by torque ripple. Therefore, the optimization method proposed in this paper can be an effective tool for the optimal design of high-performance motors, including stepper motors.