Background: The spatial orientation rules of the important skull base structures are essential for performing endoscopic surgery. However, there is no satisfactory three-dimensional (3-D) anatomy study available to the surgeon at present. The aims of this study are to construct a new method to learn the spatial orientation of anatomical features under endoscopy and to help the surgeon establish a 3-D image of skull base structures in his mind. Methods: A modified MicronTracker navigation system was used to measure the pitch angle, direction angle and distance from the reference points to various anatomical landmarks of the pterygopalatine fossa and related structures (PPFRS) at the skull base in 10 fresh cadavers (20 sides). Results: The location data of the positions of the major landmarks were acquired and a digital model of the anatomical structures of the PPFRS was built, which can be moved, whirled or demonstrated easily. Conclusion: It is practical to measure the positions of the anatomical structures of the PPFRS with a modified binocular vision-based MicronTracker navigation system. It is a valuable exploration tool to help the surgeon establish the orientation of surgical landmarks in his mind by the 3-D parameters and model.