Objective The research on vortex structure and vortex evolution in human upper respiratory tract can help to deepen the understanding of the characteristics of the airflow in human upper respiratory tract, which could give some very important assist in analyzing the diffusion, transition and deposition patterns of aerosol in human upper respiratory tract. Methods Large eddy simulation was used to simulate the vortex structure and vortex movement in human upper respiratory tract under the condition of low intensive respiratory patterns, and the vortex structure and vortex evolution in mouth throat model and in trachea triple bifurcation were discussed. Results Jet formations from airflow in pharynx and laryngeal led to two vorticity growth regions; flat vortex appeared in the throat; a curved vortex like the trachea wall appeared in the anterior wall of trachea, and nearly symmetric reverse vortex pairs appeared in the trachea; the vorticity in the G0 trachea end extended from the trachea wall to the center of the trachea, and moved to the G1 bronchial; the vorticity in bronchial of every class presented an asymmetric distribution. Conclusions The vortex structure and vortex evolution are the remarkable characteristics of the airflow in human upper respiratory tract, and the geometric airway characteristics is the main factor that results in the transformation of variable sizes of vortex structures.