Abstract: The molten pool behavior of electron beam welding was analysed in order to have a further investigation on the mechanism problems. Based on the theoretical analysis of the the molten pool of electron beam spot welding and boundary layer theory, the flushing effect of liquid metal was mathematically modeled. A three-dimensional transient model was employed to simulate the molten pool in electron beam spot welding based on finite volume method, and the influence of liquid metal flushing effect on temperature field and flow field of molten pool were discussed. The simulation results showed that the liquid metal flushing effect played an important role in temperature field of molten pool, stability of keyhole, flow field of molten pool and position of solid liquid interface. The simulated fusion line of the weld bead follows a good agreement with the experimental result, approving the validation of the mathematical model.