The invention discloses a positioning device and method for a natural head position of a virtual skull model, and belongs to the technical field of clinical medicines. The positioning device comprises an arc-shaped surface bow, a plurality of electromagnet automatic tracing pens and a plurality of supports; and the arc-shaped surface bow is fixed at the top ends of the multiple supports, the heights of the supports can be adjusted, and the multiple electromagnet automatic tracing pens are uniformly fixed on the arc-shaped surface bow. Before use, the pen points of the automatic electromagnet tracing pens are coated with X-ray developing paste, pen cores are compressed after being powered on, during use, a patient is advised to be adjusted to a natural head position state, the arc-shaped surface bow is adjusted to the height of a lower orbital plane of the patient, and the pen points are one centimeter away from the skin; and the power is cut off, the pen cores are popped out by a spring, the electromagnet automatic tracing pens extend and trace mark points capable of being developed under X rays on the lower part of the orbital of the patient, and natural head position recording is completed. The application of the device for accurately determining the natural head position of the virtual head model provides more accurate and scientific guarantee for determining the natural head position of the virtual head model during preoperative digital design of orthognathic surgery.