Obstructive sleep apnea syndrome (OSAS) is characterized by recurrent collapses of the upper airway, which lead to repetitive transient hypoxia, arousals and finally sleep fragmentation. Both anatomical and neuromuscular factors may play key roles in the pathophysiology of OSAS. The purpose of this paper was to study the control mechanism of OSAS from the mechanical point of view. A three-dimensional finite element model was developed, which not only reconstructed the realistic anatomical structure of the human upper airway, but also included surrounding structures such as the skull, neck, hyoid, cartilage and soft tissues. The respiration process during the normal and apnea states was simulated with the fluid-structure interaction method (FSI) and the computational fluid dynamics method (CFD). The airflow and deformation of the upper airway obtained from the FSI and the CFD method were compared and the results obtained under large negative pressure during an apnea episode were analyzed. The simulation results show that the FSI method is more feasible and effective than the CFD method. The concave configuration of the upper airway may accelerate the collapse of the upper airway in a positive feedback mechanism, which supplies meaningful information for clinical treatment and further research of OSAS.