A three-dimensional(3D) Monte Carlo simulator for boron ion implantation into <100>single-crystal silicon considering the mask structure has been developed to predict the mask-dependent impurity doping profiles of the implanted boron at low energies into the reduced area according to the trend of a reduction in the size of semiconductor devices. All relevant important parameters during ion implantation have been taken into account in this simulator. These are incident energy, tilt and rotation of wafer, orientation of silicon wafer, presence of native silicon dioxide layer, dose, wafer temperature, ion beam divergence, masking thickness, and size and structure of open window in the mask. The one-dimensional(1D) results obtained by using the 3D simulator have been compared with the SIMS experiments to demonstrate its capabilities and confirem its reliability, and we obtained relatively accurate 1D doping profiles. Through these 3D simulations considering the hole structure and its size, we found the mask effects during boron ion implantation process.