The China Fusion Engineering Test Reactor vacuum vessel has strict tolerances requirements and a large number of fully penetrated joints in the manufacturing and assembly processes. As the most complicated component of vacuum vessel, port stubs have stricter tolerance requirements, to guarantee the high assembly accuracy with the vacuum vessel. Due to the small deformation of electron beam welding, this method is adopted for the welding of port stub. However, welding deformation cannot be avoided, thus it is necessary to carry out finite element analysis to analyze and control the welding deformation of the port stub. In this paper, based on thermo-elastic–plastic theory, the double ellipsoid and cone-shaped hybrid heat source can accurately outline the electron beam weld pool contour of the 316L stainless steel with 50 mm thickness, which is further verified by the welding process experiment. The above hybrid heat source is applied to analyze the welding deformation of the lower port stub, and according to the deformation simulation results, the welding fixture is designed to reduce the welding deformation. The welding deformation analysis can effectively provide theoretical data support and practical guidance for the actual electron beam welding process of port stub.