Obstructive sleep apnea (OSA) is a medical condition characterized by repetitive partial or complete occlusion of the airway during sleep. The soft tissues in the airway of OSA patients are prone to collapse under the low pressure loads incurred during breathing. A numerical tool suitable for simulation of air-tissue interactions with patient-specific upper airway geometries has been developed. The tool is designed to utilize non-body-fitted Cartesian grid to avoid grid generation and remeshing processes for the deforming irregular geometries. A sharp-interface embedded boundary method is used resolving the airflow in the airway geometries, while a novel cut-cell non-linear finite element analysis is constructed for structure undergoing large deformation. The separate fluid and structure solvers are strongly coupled with a partitioned iterative algorithm. The interface is represented with the signed distance function in the flow and structural solvers. Also, the explicit interface representation with the union of Lagrangian triangle elements is introduced to manage the data exchange between two solvers. The simulation of deformation of cantilever beam under uniformly distributed load demonstrated the ability of the structural solver. The capability of the developed tool dealing with flow induced deformation problems has been exhibited with several two- and three- dimensional validation cases. To obtain the patient-specific airway and soft tissue geometries, a procedure by which patient-specific airway geometries are segmented and processed from dental cone-beam CT scans into signed distance fields is presented. The results are shown for three-dimensional flow simulation inside two rigid patient-specific airways. The simulation results of fluid--structure interaction of the pressure driven flow surrounded by deformable soft palate and tongue structures are also presented.