BACKGROUND: To measure the actual moving direction and displacement of the root and crown of maxillary teeth before and after treatment in molar distalization cases using clear aligners(CAs). MATERIALS AND METHODS: This retrospective study included 28 adult patients who received maxillary distalization treatment with CAs. The pre- and post-treatment CBCT were superimposed and the crown and root of all maxillary teeth were marked. Achieved and predicted three-dimensional displacement of maxillary teeth were then compared using the paired t test. Mixed-effect model was used to explore the influence of different staging design (one-molar distalization vs. two-molar distalization) and anchorage (TAD vs. Class II elastic vs. no extra anchorage management). RESULTS: Labial displacement happened to the anterior teeth even the palatal displacement was prescribed. Body distalization of maxillary posterior teeth could not be fully achieved as predicted. The premolars and molars achieved greater distal tipping, buccal inclination, and less distal displacement than predicted. In buccal-palatal dimension, the greatest buccal tipping tendency happened to the 2nd premolar and decreased toward the distal portion of the aligner. In the mesial-distal dimension, the highest accuracy of molar distalization was found in the 2nd molars while the lowest in the 1st premolars. No significant difference was found between two molar distalization patterns. Extra anchorage management devices could not diminish the difference between the predicted and achieved displacement. CONCLUSIONS: The achieved molar distalization displacement and anterior teeth retraction is not as good as expected using CAs. The anterior and posterior anchorage loss cannot be completely avoided despite extra anchorage management devices are adopted. The potential reason for the correction of class II malocclusion needs further exploration.