Abstract: Mass spectrometry has been widely used in the fields of chemistry, biology, environmental science, pharmacy, space exploration and so on. However, due to the long research and development cycle and high application cost of mass spectrometer, numerical simulation has become an ideal choice for mass spectrometer research, performance optimization and experimental scheme design. At present, three ion trajectory simulation software of SIMION, Comsol and Axsim have been widely used for numerical simulation and theoretical study of mass spectrometry. Therefore, the comparative analysis of these three software is important for the design of mass analyzer. In this study, the simulation process and simulation results of these three software programs were compared through the graphical user interface and operation platform, electrode modeling and electric field calculation, condition definition and program loading, ion trajectory calculation and time step selection, etc. It could be seen that the differences can complement and verify each other. The simulation results of the three software can be observed that the motion trajectory deviation position is mainly located in the ion motion direction change, and the deviation of Comsol and SIMION simulation trajectory is the largest. However, the difference in the positions of the spectral peaks between the Axsim and SIMION simulations is less than 01%. In conclusion, SIMION software is suitable for theoretical simulations of ion trajectories in complex mass spectrometry devices. Comsol has the most sophisticated graphical user interface and detailed numerical simulation modules, but it does not have special modules for spectral analysis of ion trajectories, phase analysis, etc., and the closed software program cannot be flexibly adapted to specific situations. Axsim has the most professional ion trajectory analysis program for mass spectrometry, it can intuitively guide the design of mass analyzers, but it does not have modeling and electric field calculation modules. This study can accelerate the process of numerical simulation in mass spectrometry research, and also can provide a reference for the development of domestic mass spectrometry numerical simulation software with independent intellectual property rights.