Optical navigation method cannot be used in partial craniofacial surgery due to light blocking. At present, electromagnetic navigation method can be used instead. The occlusal splint obtained from the patient's dental mold is used in the traditional electromagnetic navigation registration. Then, marker points are selected manually for registration through imaging data during the operation, which leads to the deviation of selection. In this study, the self-developed registration software was used to perform automatic registration in the intraoperative registration. Experimental results showed that it has higher accuracy and faster speed, and is suitable for the actual operation process in clinical environment compared with the traditional manual registration.