Objective To investigate upper arch changes after magnetic palatal expansion(MPE) in three-dimensional direction. Methods 15 patients treated with MPE were included in the study. Spiral CT images were used to evaluate three-dimensional changes of upper arch, and the changes of upper arch points were measured. The results were analyzed based on pairs signed rank test method. Results Upper arch and teeth move in three-dimensional changed after MPE. Upper first molars and first premolars had buccal inclination and bodily movement. The maximum expansion was observed between upper first premolars, and upper central incisors moved downward and forward. Conclusion Spiral CT is useful in the three-dimensional evaluation of maxilla after MPE and provided the first evidence to study mechanism of MPE.