Protraction of mandibular bilateral second molars to substitute for the extracted first molars is challenging in clear aligner treatment due to biological and biomechanical limitations. This case report presents a 28-year old female patient with poor prognoses for the mandibular bilateral first molars, a mesially impacted mandibular left third molar, and crowding in both the upper and lower arches. After the extraction of mandibular bilateral first molars, long-distance mandibular molar protraction was achieved using clear aligners with a novel protraction appliance, “the long arm hook”. At the end of the treatment, a Class I canine and molar relationship and good root parallelism were achieved. The combination of long arm hooks and clear aligners has proven to be clinically effective for the protraction of mandibular molars, thereby expanding the scope of clear aligner treatment.