The use of an optical see-through head-mounted display (OST-HMD) in augmented reality (AR) has significantly increased in recent years, but the alignment between the virtual scene and physical reality is still a challenge. A fast and accurate calibration method of OST-HMD is important for augmented reality in the medical field. We proposed a fast online calibration procedure for OST-HMD with the aid of an optical tracking system. Two 3D datasets are collected in this procedure: the virtual points rendered in front of the observer's eyes and the corresponding points in optical tracking space. The transformation between these two 3D coordinates is solved to build the connection between virtual and real space. An AR-based surgical navigation system is developed with the help of this procedure, which is used for experiment verification and clinical trial. Phantom experiment based on the 3D-printed skull is performed, and the average root-mean-square error of control points between rendered object and skull model is [Formula: see text]mm, and the time consumption of the calibration procedure can be less than 30s. A clinical trial is also conducted to show the feasibility in real surgery theatre. The proposed calibration method does not rely on the camera of the OST-HMD and is very easy to operate. Phantom experiment and clinical case demonstrated the feasibility of our AR-based surgical navigation system and indicated it has the potential in clinical application.