The laser welding test was carried out on AZ91 magnesium alloy with thickness 1.8 mm and 6016 aluminum alloy with thickness 1.2 mm. By using 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, 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, 12.79MPa, respectively.The hardness in magnesium and aluminum side is both higher than that of the based material, shear fracture is relatively flat and smooth, parallel fatigue crack appears.Tensile fracture has more cleavage step with brittle fracture characteristics. The main phase,such as Mg17Al12, Mg2Al3, can be found in magnesium and aluminum weld interface, Mg17Al12 brittle phase is stable than that of Mg2Al3 with ductility at high temperatures, which lead to the welded joints brittle and is difficult to realize the welding between magnesium and aluminum.