3D/3D medical image registration has important clinical significances and medical value, especially to the operation navigation and lesion location in brain surgery, the different modal 3D image data of patients need to be registered so that the medical characteristics of target tissue can be analyzed more completely and accurately. On the basis that classical registration methods are researched, the classical registration methods are embedded in Clifford algebra space, and the Geometric elements during registration calculating and the translation operator Geometric rotation operator during registration operation are built in Clifford algebra space. Then the floating image is operated with corresponding operator to achieve multimodality 3D medical image registration in head and skull. This registration method is applied to two famous 3D medical data base in the world. The experimental result indicates that this method not only inherits the advantage of classical registration methods, but also has high registration precision and intuitive geometric meaning, reducing the computing time.