Objective: To compare the three-dimensional (3-D) movement of maxillary teeth in response to three common miniscrew anchorage systems in extraction patients with maxillary dentoalveolar protrusion.Materials and methods: The study employed a randomized controlled single-blinded design with three arms. Thirty extraction patients who required maximum anchorage to retract maxillary anterior teeth were included and randomly allocated into three treatment groups: space closure with direct miniscrew anchorage and low crimpable hooks (DL group), indirect miniscrew anchorage and low crimpable hooks (IL group), and direct miniscrew anchorage and high crimpable hooks (DH group). Cone beam computed tomography (CBCT) images of all included patients were obtained immediately before (T0) and after (T1) space closure. The outcomes were 3-D positional changes of maxillary central incisor, lateral incisor, canine, second premolar, and first molar. The repeated measures analysis of variance with post hoc LSD test was used to evaluate differences among groups.Results: A significant intrusion (- 1.34 mm; 95% CI, - 1.60 mm, 1.08 mm) and buccal (- 6.92 degrees; 95% CI, - 8.67 degrees, - 5.13 degrees) and distal (4.90 degrees; 95% CI, 3.75 degrees, 6.04 degrees) inclination of the maxillary first molars were observed in the DL group, compared to the other two groups. The mesial movement (- 0.40 mm; 95% CI, - 0.83 mm, - 0.03 mm) of the maxillary first molars was found in the IL group, while the DL (0.44 mm; 95% CI, 0.15 mm, 0.73 mm) and IL (0.62 mm; 95% CI, 0.28 mm, 0.96 mm) groups exhibited distal movement. In the DH group, the lingual inclination changes of maxillary central incisor (5.04 degrees; 95% CI, 2.82 degrees, 7.26 degrees) were significantly lower, which is indicative of good lingual root torque control of the maxillary anterior teeth.Conclusion: Three miniscrew anchorage systems produced significantly different 3-D maxillary tooth movement. The maxillary first molars were significantly buccally and distally inclined and intruded in patients using direct minis crew anchorages with low crimpable hooks. Direct miniscrew anchorages with high crimpable hooks could help to achieve better lingual root torque control of the maxillary incisors.