Objective Based on computational fluid dynamics (CFD) method, the air and aerosol transport in a single alveolus were simulated to study the characteristics of airflow and aerosol transport in deep alveolus. Methods A long straight duct with a hemispherical wall at one end which had periodic expansion/contraction were regarded as simplified approximation of a single alveolus. Based on this, a two-dimensional (2D) mathematical model was established.The Euler-Euler method was used to solve the transport equations of airflow and aerosol particles in the alveolus considering air diffusion along the hemisphere boundary. Results The composition ratio of the air in the duct changed in a stable periodic way during the whole breathing process.The aerosol transport in the duct mainly depended on the particle diffusion coefficient. The advection transport had only a small effect on it. The diffusion velocity and depth of aerosol increased when the particle size decreased, especially when the particle size was smaller than 4 μm. The increase of respiratory frequency and amplitude could significantly improved the transport capacity of aerosol particles. Conclusions In atomization treatment, aerosol particles with smaller particle size have better transportation and curative efficacy. Deep breathing should be encouraged to improve particle transport.