Orthognathic surgery necessitates precise occlusal alignment during surgical planning, traditionally achieved through manual alignment of physical dental models as the recognized gold standard. This study aims to evaluate the efficacy of mixed reality technology in enhancing surgical occlusion setting compared to traditional physical alignment and an established virtual method, addressing the research question: Can mixed reality technology improve the accuracy and efficiency of occlusion setting in orthognathic surgery planning? This experimental study compared the surgical occlusion settings of 30 orthognathic cases using three methods: a new virtual method with mixed reality technology, the traditional gold standard of physical alignment, and an established virtual occlusion method using the IPS Case Designer (KLS Martin SE & Co. KG, Tuttlingen, Germany). Results indicated that surgical occlusions set with mixed reality technology were comparable to the conventional method in terms of maxillary movement and occlusal relationship. Differences observed were within the inter-observer variability of the gold standard. Both virtual methods tended to position the maxilla more anteriorly, resulting in fewer occlusal contacts. However, virtual occlusion demonstrated clinical applicability, achieving an average of 11 occlusal contacts with a bilaterally symmetrical distribution along the dental arch. The mixed reality environment provides an intuitive and flexible experience for setting surgical occlusion, eliminating the need for costly 3D-printed physical models or the automatic calculations required by other virtual occlusion methods, thereby offering maximum freedom. As a novel form of virtual occlusion, it presents a comprehensive tool that contributes to a timely and cost-effective full digital workflow of orthognathic surgery planning.