Abstract: The design and optimization of ion trap mass spectrometers equipped with continuous atmospheric pressure interfaces require a thorough understanding of ion transport from atmospheric pressure to high vacuum (~0.05 Pa). During this process, ions undergo a complex transition from continuum flow at high pressure to rarefied flow at low pressure, in which their motion is governed by the coupled effects of gas dynamics and applied electric fields. Accurately modeling ion motion across flow regimes remains a significant challenge, as traditional single-method numerical approaches often fail to remain physically valid across the entire range of Knudsen numbers ( Kn ). In this study, a comprehensive and experimentally validated multiphysics simulation framework was developed to model ion transport from continuum to rarefied flow regimes within a custom-built linear ion trap mass spectrometer. To bridge the gap between distinct flow states, a hybrid Computational Fluid Dynamics (CFD)-Direct Simulation Monte Carlo (DSMC) approach was employed. The continuum flow field in the high-pressure region was resolved using a CFD solver (ANSYS Fluent) based on the Navier-Stokes equations, while the rarefied gas flow was simulated using a DSMC solver (implemented within OpenFOAM), with the interface between the two regimes defined by a gradient-length Knudsen number criterion. Key physical quantities (gas velocity, absolute pressure, and static temperature) were interpolated from the CFD results and used as the initial and boundary conditions for the DSMC computational domain, ensuring a physically consistent transition. The resulting gas flow field was subsequently coupled with a time-dependent electric field model. By optimizing electrode voltages in accordance with the instrument’s operational timing sequence, we obtained complete ion trajectories. This enabled a detailed analysis of ion focusing, transmission, and extraction behaviors. The simulation results demonstrate that gas flow assistance plays a critical role in governing ion dynamics. The framework was validated by comparing simulated ion extraction trends with experimental signal intensities acquired from pure toluene samples. The high degree of consistency between simulation and experimental results confirmes the reliability of the developed method. While the current study utilized a simplifis 2D axisymmetric model, it establishes a robust methodology for cross-regime ion transport analysis. Future work will focus on extending the approach to fully three-dimensional simulations to further improve the accuracy of rarefied flow modeling and achieve better agreement with experimental results. In conclusion, this study proposes a multiphysics simulation method for ion trap mass spectrometers, providing a powerful visualization tool for ion trajectory analysis. This framework serves as a valuable tool for the continued development and structural optimization of ion trap mass spectrometers.