<p>Time-of-flight secondary-ion mass spectrometry (TOF-SIMS) is a powerful molecular imaging tool used in biomedical research. To overcome the low yield of non-fragmented molecular ions obtained by conventional (keV) SIMS, a novel SIMS method using MeV heavy primary ions (MeV-SIMS) has gained increasing scientific attention in recent years. We intend to develop an MeV-SIMS setup with a capillary microprobe system based on the 3 MV tandem accelerator as the first MeV-SIMS system in China. Instead of conventional magnetic or electrostatic lenses, a tapered glass capillary is used to collimate the ion beam in this device. To verify the feasibility of collimating or focusing MeV heavy ions using this capillary, understanding the main physical behaviors of MeV heavy ions interacting with the capillary is crucial. In this study, a Monte Carlo simulation program based on the Stopping and Range of Ions in Matter software is developed. The calculated energies and trajectories of heavy ions (e.g., I ions) are less affected by scattering, and both the scattered ions and recoil atoms ejected from the capillary are well separated from the direct beam in the target area. Under multiple scatterings, the contribution of the first scattering predominates. These results indicate that the capillary exhibits better collimation for heavy ions. In addition, the transmission of direct beams at different air pressures is observed. Heavy ions lose less energy at the same pressure; however, their trajectories are more divergent. The direct beam ions are not affected by the scattered ions at 100 Pa, making it feasible to perform MeV-SIMS analysis under ambient pressure.</p>