Abstract: Addition of Sc is capable of greatly improving the mechanical properties of aluminum alloy welded joints, reducing the hot crack sensitivity coefficient; thus, it could solve the welding problem of ultra-high strength aluminum alloys. Friction stir welding has the advantages of small heat-affected zone, low residual stress, and small deformation of welding work piece, making it a good choice for welding materials with high heat crack sensitivity. In this article, the microstructure and properties of friction stir welding (FSW) joints of Al–Zn–Mg–Cu–Zr–(Sc) alloys were characterized via optical microscopy (OM), transmission electron microscopy (TEM), micro-hardness testing, and universal tensile testing. The mechanism of the effect of adding Sc element on improving the welding properties of the ultra-high strength Al–Zn–Mg–Cu–Zr alloy was explored. The results show that the welding joints of Al–Zn–Mg–Cu–Zr–(Sc) alloy exhibit similar microstructure characteristics. The welding nugget zone (WNZ) displays a dynamic recrystallization feature comprising fine and uniform equiaxed grains with high density dislocations. Most of the aged precipitates dissolve into the matrix in the WNZ. The grains in the thermal-mechanical affected zone (TMAZ) are elongated with higher dislocation density, and residual aged precipitates coarsened remarkably. The heat-affected zone (HAZ) retains the same grain morphology as the base metal. Most of the aged η' precipitates grow, and a few coarsen to be the η phase in this zone. However, 0.17% (mass fraction) Sc addition increases the ultimate tensile strength of FSW joint by 43 MPa, yield strength by 23 MPa, elongation by 2.3%, and the welding coefficient up to 74.1%. Al₃(Sc, Zr) dispersoids are found to achieve the following: 1) strongly inhibit the movement of dislocations, sub-grain boundaries, and grain boundaries; 2) significantly refine grains while retaining several sub-structures; and 3) factor in Orowan precipitation strengthening. Therefore, the mechanical properties of FSW joints can be improved using the refined grain, sub-structure, and precipitation strengthening mechanisms.