Lavatories are frequently used facilities, especially on long-haul flights. Flushing a vacuum toilet in a lavatory can induce strong airflow, produce aerosols in the toilet bowl, and resuspend deposited particles from the floor. However, the exact particle transport routes and the fates of particle after toilet flushing are unclear so far. This investigation used computational fluid dynamics (CFD) to model the transient airflow and pollutant transport after a toilet flushing process in a lavatory of a commercial aircraft. The time-varying pressure profile measured in a laboratory was assigned to the drainage valve as boundary conditions. The aerosols generated inside the toilet bowl during flushing and the particles resuspended from the lavatory floor were used as particle sources. Lagrangian tracking of airborne particles in the lavatory was conducted. In addition, ammonia gas was used to examine odor perception. The multi-physics software program COMSOL 5.4 was employed for numerical solution after being validated. The results revealed that more than 70% of the generated particles in the toilet bowl are drained into sewage. A few particles may leak out of the toilet bowl and remain suspended in the air for more than five minutes when the toilet lid is open during flushing. Flushing the toilet with a closed lid can effectively reduce the particle leakage and the spread of odor gas, but it leads to greater deposition of particles on both the lid and seat. There is a slight inhalation exposure risk in the initial three minutes after flushing with a closed lid.