Magnetron sputtering is an important technology for the preparation of optical, electronic, and mechanical coatings. In these applications, deposition uniformity has a significant impact on the film properties and performance of the devices fabricated by the film. Due to the ion bombardment, the target atoms, namely, the sputtered particles, are emitted to the background gas and finally deposited on the substrate. The film deposition uniformity, therefore, is significantly influenced by the particle transportation process. In this study, a particle transport model was proposed based on MC simulation in COMSOL to analyze the effects of working conditions and geometry parameters on deposition uniformity. It is concluded that the increase in pressure and the decrease in temperature can improve deposition uniformity. Then, the influence of geometry parameters of the triple-target magnetron co-sputtering system is further investigated on the deposition efficiency and deposition uniformity. It is found that the geometry parameters determine the zone with high particle deposition. The closer the zone is to the substrate center, the higher the deposition efficiency. The greater the particle concentration difference on the substrate, the lower the deposition uniformity. Moreover, the optimized parameters were obtained to maximize both the deposition efficiency and deposition uniformity.