In this paper, a novel friction stir welding tool with shoulder at the top of the needle is developed to solve the problems in aluminum/magnesium friction stir lap welding. Based on the structural design of the shoulder at the end of the needle, the temperature difference in the thickness direction of the joint was coordinated, and the aluminum-magnesium dissimilar lapping joint was successfully prepared in two kinds of lapping methods. Taking die cast AZ31B magnesium alloy and extruded 6061 aluminum alloy as the research object, the defects and microstructure of weld joint were observed and analyzed by optical microscope and scanning electron microscope. Additionally, their mechanical properties were also evaluated. The results show that a good metallurgical reaction is formed between aluminum and magnesium, and with the increase of the effective plate thickness and the decrease of the effective lap width, the unique hook defect shape of lap welding is optimized, which also promotes the improvement of the mechanical properties of the weld. In the tensile shear experiment, it is found that the tensile shear property is improved due to the change of the shape of the hook defect, and it is a mixed fracture of toughness and brittleness.