The influence of microstructure on the mechanical properties of 6061-T6 aluminum alloy and AZ31 magnesium alloy FSW joints was studied by changing Z-axial force. The results show that, when the Z-axial force is 28kN, the ultimate tensile strength of Al/Mg joints can reach 168MPa. The intermetallic compound layer at the interface is the thinnest, and there are no irregular intermetallic compounds in the severely deformed zone; The mechanical properties of the joints decrease with the increase of Z-axial force. With the increase of Z-axial force, the heat input in the welding process increases, resulting in thickening of intermetallic compound layer at the interface, the irregular structure appears in severely deformed zone and the hole-like defect appears at the upper part of the interface, which reduce the strength of the joints.