Friction stir lap joints of LY12 aluminum alloy plates with a thickness of 3 mm were fabricated using several tools with different pin profiles. The effects of tool pin profile on the interface migration of friction stir lap joints were investigated with the comparison of weld morphologies. The results show that the screw thread of the pin plays an important role in the migration of weld interface in the thickness direction. The interface between the sheets will move upwards to the top of the plate when the pin with left hand thread was used. Conversely, the interface will move downwards to the tip of the pin when the pin with right hand thread was used: As for a stir pin with smooth surface was used, the upward or downward migration of the weld interface was largely reduced, but the extension of weld interface to the weld center line from the retreating side becomes more serious. By analyzing the force on the pin according to the sucking-extruding theory for the weld formation, the obtained results have been well explained.