In recent years, three dimensional imaging registration has been developed rapidly in clinics. Medical image registration plays an important role in the research of orthodontic image processing field. In this study, we Introduce the applications of CT registration on several clinical cases. After the registration of the pre- and post-treatment CT data, the position changes of teeth and the modeling of alveolar bone and the adaptive changes of soft tissue can be assessed precisely respectively. The three dimensional registration provides us a new and precise method to study the outcome and mechanism of orthodontics. And more studies of three dimensional registration should be performed to promote three dimensional oral medical assessment researches.