The concept of three-dimensional (3D) shave-off secondary ion mass spectrometry (SIMS) is that enables to obtain the depth information of the sample simultaneously with the mass information using the vertical axis of a two-dimensional position-sensitive detector in the mass analyzer. In this study, we simulated the trajectory of secondary ions sputtered from a virtual sample in the 3D shave-off SIMS system and investigated the magnification ratio of the ions. The simulation results showed that we could distinguish the depth position of the secondary ions sputtered from a sample by the detected position in our concept of 3D shave-off SIMS.