In order to meet the calculating requirements of high speed and miniaturized turbomolecular pump (TMP), a new modeling method is proposed for a rotor-stator row. In the same Cartesian coordinate system, the analytical equations of blade row are derived according to the real three-dimensional geometric model. A self-defining procedure is written to simulate the flow of gas molecules in TMP based on test particle Monte Carlo method. The procedure not only can calculate transmission probability of rotor row, stator row and a rotor-stator row but also evaluate the pumping performance of different blade parameters. The simulation results and known experimental data have a good agreement to confirm the feasibility of presented modeling method. The flow analysis shows that molecules at outlet of rotor row tend to accumulate in large radius and this phenomenon is obvious for high rotational speed. The differences were found between a single-stage row and a rotor-stator row. In rotor row, the molecular density at the rear blades is the highest. This is beneficial for pumping speed of TMP because 57% of molecules at the rear blades are likely to reach outlet. This will provide a direction for the structural optimization design of the blades in the future. In stator row, the molecular density reaching outlet does not significantly increase with the increase of blade velocity ratio, which indicates that the stator row is mainly used to increase the pressure ratio of TMP. The analysis of molecular density in each region reveals the pumping mechanism of TMP.