Abstract: Knudsen pump is a kind of micro-pump where gases flow from the low temperature side to the high temperature side induced by thermal creep effect, based on the micro-scale condition. In order to investigate the influence of the gas species and molecular model on the transmission characteristics of gas in the micro-channels of Knudsen pump, the method of Direct Simulation Monte Carlo (DSMC) is applied to investigate the classic rectangular micro-channel. The variations of three kinds of gases (Ar, N₂ and O₂) and three kinds of molecular models (HS, VHS and VSS) are considered respectively under the condition of different working pressures. From the research, it is found that different kinds of gas species and molecular models will not lead to the obvious change of the macroscopic flow field in the micro-channel. For the gases with a light molecular mass have a stronger thermal creep effect, and the maximum thermal creep effect corresponds to a large pressure. Regarding to molecular model, the thermal creep effect is the strongest for VHS model while the thermal creep effect is the weakest for HS model. Therefore, compared with VSS model which could reflect moving rules of the real gas molecules better, application of VHS model will overestimate the performance of pump but underestimated by using HS model.