Background <p>Bilateral scissor bite is a rare malocclusion. For adult patients with skeletal disharmonies, orthognathic surgery is usually adopted for correction. Non-surgical orthodontic treatment is more difficult and rarely reported. During orthodontic treatment, it is necessary to reposition malpositioned molars. However, in some patients, excessive pneumatization of the maxillary sinus allows the molar roots to extend into the sinus cavity. This significantly increases the difficulty of moving the molars.</p> Case presentation <p>This case reports an adult patient with transverse maxillary hyperplasia, bilateral scissor bite, deep overbite, mandibular retrusion, and deviation. Additionally, due to excessive maxillary sinus pneumatization, the roots of the maxillary molars were located within the maxillary sinus. In this case, mini-implants were used in combination with palatal long-arm traction hooks of the first molars. Concurrently, the maxillary second molars were extracted, and the third molars were used as replacements. Following 45 months of treatment and a 12-month retention period, the patient displayed a normal overbite and overjet, proper molar relationships, improved facial aesthetics, and a healthy temporomandibular joint.</p> Conclusions <p>This case demonstrated that bodily movement of the tooth through the maxillary sinus can be achieved by using suitable force systems, correcting the bilateral scissor bite caused by transverse maxillary hyperplasia and avoiding surgical damage and complications.</p>