The impact mechanisms of the thermal effect of vacuum electron beam welding on the micro-hardness of AZ91D and AZ31B magnesium alloy weld were studied. The experiment results showed that the welding thermal effect exerts its influence on weld hardness differently for AZ91D and AZ31B magnesium alloy. Two factors affecting the micro-hardness of the weld should be included, which are the cooling rate after welding and the burning loss of alloying elements after the action of welding thermal effect. When the welding heat input is large, the main factor affecting the weld hardness of AZ91D magnesium alloy is the increase of strengthening phases because of the burning loss of Mg elements. A larger welding heat input induces more strengthening phases in weld and the weld hardness increases relatively. When the welding heat input is small, the main factor affecting the weld hardness of AZ31B magnesium alloy is the cooling rate after welding. The smaller welding heat input induces faster cooling and solidification rate after welding and then forming fine grains, so the weld hardness is relatively high.