The heat treatment of friction stir tailor-welded aluminum joints is one important key process to improve the efficiency of joint strength and ductility as well as fracture locations, since almost all of the welded parts are subjected to a forming process. Therefore, the effect of heat treatment on microstructural characterization and mechanical properties of welded joints is a very important research area to improve the nugget zone in welded structures of aircraft segments. The objective of this study is to investigate the effect of changing pre-weld heat treatment conditions (first case: solution heat treated with artificial aging (T6) and second case: annealed heat treatment (O)) by microstructural characterization with an optical microscope, scanning electron microscope and x-ray diffraction and mechanical properties using micro-hardness, tensile and bending tests. After that, ANOVA was used in order to determine the interaction effect between the conditions of heat treatment (T6 and O) and interlayer strip widths. The results revealed that the softened zone of FSW joints in the annealed condition (O) was relatively more homogeneous than FSW joints from solution heat treated and artificially aged (T6). On the other hand, the strength efficiency of FSW joints from annealed (O) samples was the higher value than the joints efficiency at solution heat treated and artificially aged (T6). Furthermore, the annealed (O) FSW joints fractured in the base metal, while FSW joints from solution heat treated and artificially aged (T6) samples fractured in the HAZ. The microstructure and mechanical properties of weld nugget zones were influenced by the pre-weld heat treatment conditions. Finally, the results of ANOVA agreed with the results of mechanical properties.