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Introduction Hyperdivergent skeletal class II malocclusion in adolescents is characterised by mandibular retrognathia with excessive vertical growth and clockwise mandibular rotation, which can worsen facial profile and airway-related morphology. Although mandibular advancement approaches are commonly used, they may increase the vertical dimension and are suboptimal for patients with long-face patterns. This randomised controlled trial aims to evaluate a micro-implant-assisted protrusion correction technique designed to flatten the occlusal plane and promote counterclockwise mandibular rotation, thereby improving facial profile and pharyngeal space.Methods and analysis This trial is registered at the Chinese Clinical Trial Registry (ChiCTR; ChiCTR2100054105). This is a two-arm, multicentre, randomised, parallel-controlled trial. Ninety adolescents will be recruited from Shanghai Stomatological Hospital, Zhongshan Hospital (Fudan University), and Xinhua Hospital (Shanghai Jiao Tong University School of Medicine), and will be randomly allocated (1:1) to the test or control group. The control group will receive conventional anterior teeth retraction, whereas the test group will receive a micro-implant-assisted vertical control protocol with occlusal plane flattening. The primary outcome is the change in the A point–nasion–B point angle. Secondary outcomes include changes in the occlusal plane, incisor and molar heights, and facial height. Measurements will be assessed at baseline, at the end of treatment and at 12 months after treatment completion.Ethics and dissemination This study was approved by the Ethics Committee of the Shanghai Stomatological Hospital (approval no. (2022)006). The results of this study will be made available in peer-reviewed journals.Trial registration number ChiCTR2100054105.