Abstract: In order to study the effect of different tool structures on the microstructure and mechanical properties of a joint, this paper carries out friction stir welding butt tests on 3 mm 6061 aluminum alloy and 304 stainless steel. The results show that, with the optimization of the tool from a cylindrical one to a conical plus threaded one, the C-type characteristics are more and more obvious. The threaded tool promotes the flow of the material in horizontal and axial directions, and the steel particles of the joint are evenly and finely distributed at the interface. The changing law of microhardness of the three joints in the welding area is similar, and the hardness in the welding area is higher when the conical plus threaded tool is used. The average tensile strength of the joint of the conical plus threaded tool is 197.2 MPa, which is higher than that of the threadless tool. It breaks at the heat affected zone on the aluminum side, and the fracture shows a typical toughness fracture mode.