Abstract: To solve the engineering challenge that pores and cracks tend to form and mechanical properties degrade in MIG fusion welded 6061 aluminum alloy for aircraft assembly tooling, friction stir welding (FSW) experiments were carried out on 10 mm thick 6061 aluminum alloy plate. The welding speed was fixed at 300 mm/min, and rotational speeds of 800 r/min and 1200 r/min were selected for comparison with MIG welded joints. The effects of rotational speed of stirring head on the microstructure evolution, grain boundary characteristics and mechanical properties of FSW joints were investigated. The results show that defect-free FSW joint is obtained at 800 r/min. Complete dynamic recrystallization produces fine equiaxed grains with an average size of 1.26 μm in the weld nugget zone. The tensile strength and elongation of the welded joint reach 302 MPa and 10.2%, respectively. As the rotational speed increases to 1200 r/min, high strain rate restrains dynamic recrystallization, the fraction of low angle grain boundaries increases and grains coarsen, leading to simultaneous deterioration of strength and plasticity. The heat affected zone becomes the mechanical weak region owing to recovery and over aging. By contrast, the tensile strength of the MIG joint is only 197 MPa due to pores and hydrogen induced defects. This work provides theoretical support for the engineering application of FSW for thick plate 6061 aluminum alloy in aeronautical tooling.