The friction stir welding process of 6 mm A356-T6 and 6061-T6 dissimilar aluminum alloy were study. And the joint organization and performance affects on welding speed and base metal position were investigated by using OM, SEM, universal tensile testing and micro hardness testing.The results show that no obvious defects and good appearance dissimilar aluminum joints could be acquire when the rotational speed of 1 000 r/min, welding speed about 100 to 400 mm/min were used. The material migration increased with welding speed decreasing, and A356 -T6 aluminum which located in advancing side was beneficial to transport materials. The joint consisted of nugget zone, thermal mechanical affected zone and heat affected zone,which are typical characterized organizations in FSW joints. The grain of weld nugget refined from surface to the bottom gradually. The tensile properties of the joints were increased with the welding speed increases. A356 alloy in the advancing side could be obtain higher strength joints at low welding speed, while higher strength were obtained at higher welding speed when 6061 in the advancing side. However,the yield strength and elongation of joint when A356 located in advancing side were higher than 6061 located in the advancing side. The fracture location of joints located in the heat affected zone of A356 side regardless of which base metal located in advancing side, and had nothing to the base metal location. And the hardness test exhibited that fracture location of joints correspond to the zone of the lowest hardness value.