To solve the problem of fusion of virtual scene and real scene of Optical See-Through Head-Mounted Display (OST-HMD) in Augmented Reality (AR), a fast calibration method for OST-HMD was proposed on the basis of optical positioning and tracking system. Firstly, the virtual makers in OST-HMD and the corresponding points in real world were collected as two 3D point datasets, and the transformation between the virtual space and optical positioning and tracking space was estimated to solve the transformation matrix from the virtual space to the real scene. Then, the transitive relation among matrices of the entire navigation system was built, and an AR-based surgical navigation system was designed and implemented on this basis, and the accuracy validation experiment and model experiment were conducted to this system. Experimental results show that the proposed algorithm makes the root mean square error between the virtual datum points and the corresponding real datum points achieved 1.39 ±0.49 mm, and the average time of calibration process of 23.8 seconds, which demonstrates the algorithm has the potential in clinical applications.