This study aimed to analyze pharyngeal airflow characteristics and their relationship with the skeletal movement of the maxilla and mandible after bimaxillary orthognathic surgery in patients with skeletal class III (mandibular prognathism) malocclusion. Cone-beam computed tomography (CBCT) was conducted before surgery (T0), immediately after surgery (T1), and at least six months after surgery (T2). Digital imaging and communications in medicine files were transferred to InVivo (Anatomage) software to measure the skeletal changes after surgery. The changes in the maxillary and mandibular position, tongue position, and hyoid bone position were analyzed. Patient-specific models were reconstructed using 3D-Doctor software. The models after converting to the stereolithography (STL) file for Ansys integrated computer engineering and manufacturing code for computational fluid dynamics (ICEM CFD), commercial software were used for calculating the geometry, pressure drop and adjusted pressure coefficient value. The total volume of the upper airway including nasal cavity was reduced by 23% immediately after surgery and recovered to 92.2% of the initial volume six months after surgery. The airflow computation analysis showed a decrease in the pressure drop values immediately after surgery and six months after surgery. The adjusted pressure coefficients were slightly different but the change was statistically insignificant. The airflow characteristics computed using the computational fluid dynamics were correlated to the surgical changes. The surgical changes can affect the aerodynamics of the pharyngeal airway. In clinical practice, this knowledge is useful for developing a suitable orthognathic surgery treatment plan.