Friction stir welding (FSW) is a solid phase process which can produce high quality dissimilar joints. However, due to the difference of material properties between A6N01 aluminum alloy and AZ31 magnesium alloy, optimization of process parameter is difficult for dissimilar FSW. In this study, the relationship between process factors (material arrangement, tool offset and probe diameter) and quality of the joint was investigated. After the optimization of these process factors, the AZ31 and A6N01 dissimilar joints with high joint efficiency could be obtained at circumferential velocity of the probe from 0.147 to 0.183m/s regardless of probe diameter. This result indicates that the circumferential velocity is one of the most important factors for AZ31 and A6N01 dissimilar FSW.