The inhomogeneity of friction stir weld (FSW) joint of a 7085 Al-based alloy containing trace Sc was investigated by comparing the hardening phase morphology, grain structure, mechanical properties and fatigue crack growth (FCG) behavior in based metal (BM), heat-affected zone (HAZ) and weld nugget zone (WNZ). The results showed that microstructural evolution during FSW was remarkably affected by Sc addition. The recrystallization and growth of grains in BM and HAZ were restrained by coherent Al3(Sc,Zr) particles. In HAZ, partially dissolution and slight growth of precipitates resulted in softening but contributed to enhance the FCG resistance according to shear mechanism. In WNZ, high frictional heating and intense plastic deformation induced recrystallization and supersaturated solid solution which decomposed to form new reprecipitates, including many new GPII zones, ′ phases and some coarse equilibrium phases attached to grown incoherent Al3(Sc,Zr). Owing to combined influences of fine random orientated grain structure and reprecipitates, WNZ possessed the best fatigue endurance.