The electron beam welding (EBW) is a highly efficient and precise welding method that have been used in the manufacturing of the port stub of vacuum vessel (VV) of Chinese Fusion Engineering Test Reactor (CFETR). The port stub is a large-scale complex double wall structure with thickness of 50mm. This work describes the numerical simulation of EBW involves the analysis of heat source model, deformation, stresses, mechanical and metallurgical phenomena. Sysweld and weld planner software are used to deal with the numerical simulation. Different heat source model are compared with weld morphology, and finally the combined heat source model is proposed to simulate EBW process. Moreover, based on inherent strain theory welding sequences are simulated to study the effect of welding sequences on the welding stress and distortion.