In this paper, the method of Taguchi method is used to determine the polearc coefficient and width of coilside, which are the main parameters that affect the fundamental amplitude and the total harmonic distortion of the noload voltage of the axial flux permanent magnet generator. The winding factor with harmonic of electromotive force (EMF) of generators was deduced in the case of considering the flux density with harmonic. The winding factor with harmonic can be controlled by the optimization of the width of coilside and polearc coefficient. By the maximum amplitude of the fundamental harmonic of the EMF and the minimum total harmonic distortion (THD) as the optimizing goal, the optimization scheme of the match between polearc coefficient and width of coilside was found by the response surface methodology, and the optimization results was proved by finite element analysis (FEA) results. After optimization, the performance of the generator was improved obviously, the reliability of the optimization methodology applied in axial flux permanent magnet machine was proved.