The 211-aperture-pair two-grid ion optics of a miniature ion thruster is numerically simulated. Since the plasma in the miniature ion thruster is too inhomogeneous to introduce mirror or translational boundary conditions between apertures, all the apertures of the grid system are considered. The simulation is self-consistent, the ion current profile in the discharge chamber plasma is given by the particle-in-cell with Monte Carlo collision algorithm calculations, and all the ion beams extracted from the full-aperture-pair array were tracked including charge-exchange ions. A scheme for the construction of the full-aperture-pair simulation domain is proposed based on the array of a six-fold hexagonal single-aperture-pair simulation domain, which can be extended to other numbers of aperture pairs. Numerical results on accel impingement current and ion-beam profile are compared to experimental data and shown to be in reasonable agreement. Furthermore, the full-aperture-pair ion-optics model is compared with the single-aperture-pair ion-optics models used in the majority of previous ion-optics simulations, which showed that the full-aperture-pair ion-optics model yielded the most accurate predictions. These results suggest that the ion thruster grid system using an inhomogeneous plasma source can be designed more accurately and effectively using full-aperture-pair ion-optics simulations.