Using the optical microscope, tensile test machine and micro-hardness meter, the effect of heat input on the microstructure and mechanical properties in fusion welding joints of AZ31B wrought alloys was investigated systematically, the mechanism on joint properties losing was analyzed, and a valid method to improve joint properties of the magnesium alloy fusion welding was explored. The results show that the heat input has an obvious effect on the microstructure and properties. Under the condition of penetration, with the heat input decreasing, the crystal grain in the weld and heat-affected zone (HAZ) becomes fine, the width of HAZ becomes obviously narrow, and the molding of the weld is improved, so the tensile strength and elongation are increased and the hardness of joints is improved. When the heat input reaches 60 J/mm, the high quality joints can be gained.