The thermal behavior during electron beam welding on magnesium alloy were analyzed and simulated. According to the thermal effect of the electron-beam-generated keyhole, a mathematic model of rotary Gaussian body heat source with incremental power-density-distribution was developed. This model can be useful for simulating the thermal effect of metal vapor plasma on the surface of the workpiece and the deep-penetrating effect of the electron beam. By the action of thermal model, the characteristics of temperature field during vacuum electron beam welding on AZ61 magnesium alloy were studied by the method of finite element analysis. And then, the influence of welding parameters on the temperature distributions and the weld contours were analyzed. The simulations and experiments showed that the different deep-penetration effects and temperature distributions were achieved with the varying welding energy inputs, and the metal vapor plasma has a significant impact on the weld contour of magnesium alloy.