Insufficient vertical space is often a great challenge for prosthodontic treatment of patients with teeth overeruption. This case report describes a simple technique using clear aligners to intrude over-erupted molars. A 27-year-old woman was diagnosed with left mandibular dentition defect, yet the left third molar was presented in lower arch. However, the prosthetic rehabilitation was limited by the opposing over-erupted molars. Clear aligners therapy (CAT) was used to regain the necessary interocclusal space. After initial molar distalization, subsequent 2.14 mm and 1.3mm intrusion for left maxillary first and second molar was designed to solve the door-wedge effect dilemma. Without mini-screws, considerable intrusion (1.9 mm and 0.9 mm for left maxillary first and second molar, respectively) was achieved within 6 months with minimal discomfort. Radiological and clinical examinations revealed a favorable occlusal relationship and improved alignment for both arches. Outcomes in the case revealed that intruding over-erupted molars via CAT may be an effective approach.