Secretions in the airways of mechanical ventilated patients are extremely dangerous to patients' health. In recent studies, the continuous constant airflow is adopted, however, it is not consistent with a clinical situation. To study respiratory airflow dynamic characteristics with secretion in the airways, a mathematical model based on clinical mechanical ventilation is established in this paper. To illustrate the secretion's influence on the airflow dynamics of mechanical ventilated respiratory system, three key parameters which are cross section area ratio of secretion/ pipe, air-secretion contact area, and secretion viscosity are involved in the study. Through the experimental study, the accuracy and dependability of the model are confirmed. By the simulation study, we find that: based on the model which combines two airways and two model lungs, when one of the airways was covered with secretion, the maximum pressure of the model lung which is attached to the end of this airway maintains constant when the cross section area ratio is less than 66 percent, and then it tends to decline sharply with the ratio increasing, but it remains constant with the augment of air-secretion contact area, the maximum flow declines both with the increasing of cross section area ratio and air-secretion contact area. Furthermore, as for the other airway, the maximum pressure of the model lung has no significant changes with the augment of area ratio and air-secretion contact area, however, along with the increasing of area ratio and air-secretion contact area, the maximum flow rises up. Moreover, the secretion viscosity has barely any influence on airflow dynamics. According to our analysis results, we conclude that the cross section area ratio of secretion/pipe has bigger influence on airflow dynamic characteristics than air-secretion contact area and secretion viscosity. This paper lays the foundation for the further study of efficacy and safety in mechanical ventilation and the secretion clearance of mechanical ventilated patients. In addition, the mathematical model proposed in this paper can also be referred to study on the secretion movement in human airways.