The laser welding test was carried out on the AZ91 magnesium alloy with thickness of 1.8 mm and the 6016 aluminum alloy with thickness of 1.2 mm. By optical microscopy, horizontal microscope, scanning electron microscopy, X-ray diffraction, electron micro-hardness and tensile test, the weld surface morphology, microstructure, interface element distribution, fracture morphology, main phase, hardness and mechanical properties of joints were studied. The results indicate that the morphology of welding surface can be improved, the heat affected zone is narrow and grain size is fine when the welding power is 1900 W, welding speed is 50 mm/s, the defocus distance is 0 mm, and Ar gas acts as the protection gas with flow rate 15 L/min. The average tensile and shear strength of the welding sample reaches 13.99 MPa and 12.79 MPa, respectively. The hardness in magnesium and aluminum side is both higher than that of the based material, shear fracture is relatively flat and smooth, and parallel fatigue cracks appear. Tensile fracture has many cleavage steps with brittle fracture characteristics. The main phase, such as Mg17Al12 and Mg2Al3, can be found in magnesium and aluminum weld interface, and Mg17Al12 brittle phase is more stable than Mg2Al3 with ductility at high temperatures, which lead to the brittle welded joints and thus it is difficult to realize the welding between magnesium and aluminum