To identify whether intramaxillary miniscrew anchorage could achieve a better maxillary arch distalization effect in clear aligner treatment compared to Class II elastics. Thirty adult patients with Class II dentition who were treated with whole maxillary arch distalization using clear aligners were collected. Either intramaxillary miniscrew anchorage (miniscrew group, n = 17) or intermaxillary Class II elastics (Class II elastic group, n = 13) were used to support maxillary arch distalization. Three-dimensional predicted and achieved displacements, and angular changes of maxillary posterior teeth and anterior teeth, were measured and compared. The achieved distalization efficiency was 36.2%-43.9% in the posterior teeth and the retraction efficiency was 36.9%-49.4% in the anterior teeth. No statistically significant differences were found in maxillary arch distalization efficiency between the groups. The miniscrew group achieved less incisor extrusion and posterior tooth distal tipping than the Class II elastic group. Both groups achieved comparable arch expansion, posterior tooth buccal inclination, and anterior tooth lingual inclination. Intramaxillary miniscrew anchorage and intermaxillary Class II elastics achieved comparable efficiency in maxillary arch distalization. However, the miniscrew anchorage showed better vertical control in anterior teeth and mesiodistal tipping control in posterior teeth.