In this study, finite element analysis (FEA) has been used to investigate the effects of different Laval nozzle throat sizes on supersonic molecular beam. The simulations indicate the Mach numbers of the molecular stream peak at different positions along the center axis of the beam, which correspond to local minimums of the molecular densities. With the increase of the throat diam-eter, the first peak of the Mach number increases first and then decreases, while that of the molecular number density increases gradually. Moreover, both first peaks shift pro-gressively away from the throat. At the last part, we discuss the possible applications of our FEA approach to solve some crucial problems met in modern transportations.