Al alloy and Mg alloy, which have advantages of low density and high specific strength, are widely applied in aerospace industry, yet easily generate brittle intermetallic compound during welding, thereby causing great difficulty in acquisition of joints with excellent performance. Therefore, during soldering, choose of soldering filler metal which can avoid generation of harmful intermetallic compound is key to acquisition of high grade Al/Mg dissimilar metal joint. In this work, Sn-based and Zn-based soldering filling metals are chosen, 6063 Al alloy and AZ31B Mg alloy are welded by ultrasonic-assisted soldering at atmosphere, and contrastive analysis is carried out to the two solder joint microstructures of soldering filler metals by OM, SEM and EDS spectrum. The results indicated that when Sn-based soldering filler metal is adopted, the joint cannot generate Mg-Al brittle intermetallic compound, Al elements which dissolve in soldering seams exist in the joint in form of Al-Sn-Zn and Ag (Al) phases, and when the ultrasonic action time reaches 4.5s, the Al elements are uniformly distributed in the whole soldering seam. When Zn-based soldering filler metal is adopted, large amount of brittle Mg/Al intermetallic compound generate in the joint, and second-phased low-melting-point Sn particles disperse at the grain boundary of the soldering seam.