In this study, preoperative planning for orthognathic surgery was performed in a virtual space. It was shown that VR simulation could provide easy handling of 3D models, for adjusting the maxilla and mandible with intuition. Orthognathic surgery was performed with an AR navigation system, which provided the operator with the preoperatively planned 3D model superimposed with the actual surgical site. The differences between the preoperative plan and postoperative 3D model were 1.18 mm at ANS, 4.22 mm at PNS, 2.05 mm at Right MxM1, 2.02 mm at Left MxM1, 2.34 mm at Pog, 4.32 mm at Right MnM1, and 4.88 mm at Left MnM1. The Mean value was 3.00 mm and the standard deviation was 1.44 mm. The deviation in our findings was measured as somewhat high. This difference is considered a depth problem; results that are more accurate can be obtained when depth cameras and optical markers are used. In the future, we need to apply haptic-related VR simulation; it will provide us with great advantages for 3D medical simulations, with accurate manipulation and immersiveness. AR navigation has great potential for medical applications; it has many advantages, including displaying a real-time augmented 3D model of the patient, and it is easily applied in the surgical field, without complicated 3D simulations or 3D-printed surgical guides.