Objective The air and aerosol transport in a single alveolus were simulated to study the characteristics of airflow and aerosol transport in deep alveolus based on computational fluid dynamics. Methods A long straight duct with a hemispherical wall at one end which has periodic expansion/contraction were regarded as a simplified approximation of a single alveolus. Based on this, a two-dimensional mathematical model was established. The Euler-Euler method was used to solve the transport equations of airflow and aerosol particles in the alveolus considering the diffusion of air along the boundary of the hemisphere. Results The composition ratio of the air in the duct changes in a stable periodic way during the whole breathing process. The aerosol transport in the duct mainly depends on the particle diffusion coefficient. The advection transport has only a small effect on it. The diffusion velocity and depth of aerosol increased when the particle size decreased, especially when the particle size is less than 4μm. The increase of respiratory frequency and amplitude could significantly improve the transport capacity of aerosol particles. Conclusion In atomization treatment, aerosol particles with smaller particle size have better transportation and curative efficacy. And deep breathing should be encouraged to improve particle transport.