Objective To study three-dimensional anatomy of the occipital condyle approach to the jugular tubercle using virtual reality system. Methods Eighteen cadaveric heads were used for the magnetic resonance imaging (MRI) and head CT scans. The scan image data input into virtual reality system which was used to build three-dimensional anatomical model in jugular hole area, design the occipital condyle approach to jugular tubercle during calvarium and skull base surgery, and analyze bony landmark observation of different surgical measurements reveal and anatomical data in comparison. Results The simulated surgery path reflected the nerves, blood vessels, and anatomical structure change along with the changes of the operating direction and angle. The results of by virtual reality systems were same as consistent body cephalometric, but the three-dimensional anatomical method did not limit about observe and the angle measure. Three dimensional anatomical imaging model showed that the surgical path volume, sinus volume in path and rock bone structure after injury were less than that before injury（P＜0.01）. There was not statistically significant difference of brain volume before and after injury（P＞0.05）. Conclusion Via occipital condyle in the minimally invasive surgery path can under the condition of the limited targets exposed anatomical structure changes, also reduce the important nerve vascular structural damage, worthy of clinical popularization and application.