Purpose: This study aimed to assess the three-dimensional (3D) facial changes after orthognathic surgery by evaluating the spherical coordinates of facial lines using 3D computed tomography (CT). Materials and Methods: A 19-year-old girl was diagnosed with class III malocclusion and facial asymmetry. Orthognathic surgery was performed after orthodontic treatment. Facial CT scans were taken before and after orthognathic surgery. The patient had a menton deviation of 12.72 mm before surgery and 0.83 mm after surgery. The spherical coordinates of four bilateral facial lines (ramal height, ramal lateral, ramal posterior and mandibular body) were estimated from CT scans before and after surgery on the deviated and opposite side. Results: The spherical coordinates of all facial lines changed after orthognathic surgery. Moreover, the bilateral differences of all facial lines changed after surgery, and no bilateral differences were zero. Conclusion: The spherical coordinate system was useful to compare differences between the presurgical and postsurgical changes to facial lines.