Abstract: Understanding the gas dynamics characteristics of the mass spectrometry (MS) ion transport system is important for improving the sensitivity of MS instruments. Based on the coupled of the Navier-Stokes equation and the Direct Simulation Monte Carlo method, the flow field characteristics of the gas from the atmospheric pressure continuous flow to the vacuum rarefied flow can be calculated. Further coupling with the electric field simulation, ions' transportation, and spatial distribution information can be obtained, and the performance of ion optical devices can be evaluated. Based on photoionization mass spectrometry, this work constructed a combined structural model of capillary injection, photoionization source, and sampling cone, established a multi-physics simulation method for ion transportation across flow regimes, obtained the effects of two types of structured photoionization source electrodes on the ion transportation efficiency, and verified the reliability of the simulation method using a self-made photoionization time-of-flight mass spectrometer. This work provides theoretical guidance for the design of mass spectrometry photoionization sources and ion transportation instruments under complex flow and electric field environments.