Treatment of sinusitis by surgical procedures is recommended only when medication therapies fail to relieve sinusitis symptoms. In this study, a realistic 3D model of the human upper airway system was constructed based on CT images of an adult male and three different virtual functional endoscopic sinus surgeries (FESS), including only uncinectomy and uncinectomy with two different sizes of Middle Meatal Antrostomy (MMA) performed on that model. Airflow and deposition of micro-particles in the range of 1–30 µm were numerically simulated in the postoperative cases for rest and moderate activity breathing conditions. The results showed that the uncinate process alone protects the maxillary sinus well against the entry of micro-particles, and its removal by uncinectomy allows particles to deposit on the sinus wall easily. Generally, uncinectomy with a degree of MMA increases the number of deposited particles in the maxillary sinuses compared to uncinectomy surgery alone. In the studied models, the highest particle deposition in the maxillary sinuses occurred among particles with a diameter of 10–20 µm. Also, if a person inhales particles during rest breathing conditions at a low respiratory rate, the number of particles deposited in the sinuses increases.