Abstract: The distribution of the thread on the pin has an important effect on the material flow behavior in the friction stir welded joint, and then affects the joint formation and mechanical properties. In order to investigate cross-section morphology, microstructure, shear failure performances and fracture position of FSLW joints, the taper-threaded pin and the stepped reverse-threaded pin were used to weld 2A12-T4 aluminum alloy. The results showed that the morphologies of joints in cross section under the two types of pins presented “bowl-shaped”. However, the unique “parenthesis” morphology appears at the retreating side of joints using the stepped reverse-threaded pin. Compared with the taper-threaded pin, the grain distribution in the thermo-mechanically affected zone and heat affected zone of the joint welded by the stepped reverse-threaded pin was not different, but the grain refinement degree of stir zone was more obvious. Meanwhile, the maximum shear failure performance was 10.39 kN at the welding speed of 80 mm/min. The “parenthesis” shape on the retreating side of the joint welded by the stepped reverse-threaded pin prevented the crack from spreading to the stir zone, and the fracture mode was tensile fracture.