Magnesium alloys are being increasingly used in automotive and aerospace structures. In this study, welding of AZ61 magnesium alloy with 10 mm thickness was carried out using vacuum electron beam welding (EBW). By using the finite element model and the 3D moving double ellipsoid heat source model, numerical simulation method was employed to study the influence of the electron beam current on the temperature field of welding process and weld penetration. The microstructure and microhardness of weld joint obtained by the optimized vacuum EBW process had been investigated in detail. The results show that the numerical simulation result basically matches the experimental result. A favorable joint had been obtained by EBW for AZ61 magnesium alloy, in which heat affected zone was not evident, the fusion zone (FZ) consisted of fine-equiaxed grain. The weld hardness was greater than that of the base metal.