Mechanical ventilation (MV) is an effective management strategy for neonates with critical congenital heart disease or congenital tracheal stenosis (CTS). However, there is no standard for patient-specific mode selection. This study numerically investigated the aerodynamic effects of tracheal model with severe stenosis when by different levels of ventilator assist during Pressure Support Ventilation (PSV) and Neurally Adjusted Ventilatory Assist (NAVA). Based on medical images, a three-dimensional (3D) tracheal model with insertion of a cuffed endotracheal tube was reconstructed. The technology of Computational Fluid Dynamics (CFD) was applied to simulate the airflow in the trachea. The aerodynamic parameters, including pressure drop (PD), streamlines and rate of energy loss (ELR), were compared to assess the MV effects. The results indicated that high assist level, accompanied by high airflow velocity, should be the main cause of aerodynamic disorders in the airway during MV. Lower PD, ELR and relatively steady velocity of NAVA was observed. Compare with PSV, it was inferred that preserved auto-regulation of respiration during NAVA may have potential advantages for flow rate regulation in patient with CTS. CFD analysis is a potential noninvasive tool for obtaining tracheal aerodynamics, which will be helpful for making decisions of appropriate MV mode.