Objective To investigate the clinical effect of micro-screw implant anchorage in the treatment of malocclusion. Methods A total of 96 patients with malocclusion who were treated in our hospital from February 2021 to April 2023 were randomly divided into reference group and study group, with 48 patients in each group. The reference group was treated with extraoral arch anchorage orthodontics, and the study group was treated with micro-screw implant anchorage orthodontics. The clinical efficacy, dentition index, masticatory function and complications were compared between the two groups. Results The total effective rate of treatment in the study group was 97.92%, which was higher than 85.42% in the reference group (P <0.05). The width of the upper incisors, the angle of the upper central incisors, the width of the lower incisors and the angle of the lower central incisors in the study group were greater than those in the reference group (P <0.05). The masticatory efficiency and bite force of the study group were better than those of the reference group (P <0.05). The incidence of complications in the study group was 2.08%, which was lower than 14.58% in the reference group (P <0.05). Conclusion The application of micro-screw implant anchorage in patients with malocclusion is effective, which can improve the clinical efficacy, optimize the dentition index, improve the masticatory function and bite force, and has high safety.