The effects of tool geometry and process parameters on the mechanical properties of friction stir spot welded (FSSW) dissimilar aluminum alloys are experimentally investigated. Two tools with different shoulder profiles, concave and convex, were considered. Two typical automotive aluminum alloys were selected for FSSW, thus resulting in two different material combinations for each shoulder profile. The experimental results showed that the two shoulder profiles caused significant differences in the axial force, the mixing of materials, and the mechanical properties of the joint. The sensitivity of joint strength to the variation of the tool rotation speed and the plunge speed was also quite dependent on the shoulder profile. The experimental result shows that the change of joint strength can be quite significant.