This paper presents a distributed winding type axial flux permanent magnet synchronous generator (AFPMSG) with reduced the total harmonic distortion (THD), suitable for wind turbine generation systems. Although the THD of the proposed distributed winding type is more reduced than the concentrated winding type, the unbalance of the phase back EMF occurs. To improve the unbalance of the phase back EMF and the output power of the distributed winding type AFPMSG, the Kriging based on the latin hypercube sampling (LHS) is utilized. Finally, these optimization results are confirmed by experimental results. As a result, the unbalance of the phase back EMF and the output power of the distributed winding type AFPMSG were improved while maintaining the total harmonic distortion (THD) and the average phase back EMF.