The Role of Clear Aligners in Orthodontic–Orthognathic Treatment: Benefits, Challenges, and Limitations Clear aligners have expanded the range of aesthetic and comfortable alternatives to fixed appliances for managing malocclusions. They are increasingly used during preoperative preparation and postoperative orthodontic treatment in patients undergoing orthognathic surgery. However, their application in complex surgical cases presents distinct biomechanical and clinical challenges. Compared with fixed appliances, clear aligners may provide less predictable control of demanding tooth movements, including root torque, extrusion, and rotation. These limitations are particularly relevant during presurgical dental decompensation, where precise three-dimensional positioning of the teeth is essential for achieving the planned surgical movements and postoperative occlusion. Refinements, auxiliary mechanics, or temporary conversion to fixed appliances may therefore be required. Occlusal management represents an additional concern. By covering the occlusal surfaces, aligners alter periodontal and occlusal sensory input and may interfere with the establishment of stable intercuspation. Reliable occlusal contacts are important for postoperative mandibular positioning, neuromuscular adaptation, and condylar stability. Consequently, postoperative settling may be less predictable and may require carefully planned wear protocols, selective use of elastics, refinement aligners, or periods without aligner coverage. Clear aligners nevertheless offer important advantages, including improved aesthetics, comfort, oral hygiene, and digital integration with virtual surgical planning. Their removable design may also facilitate perioperative care. However, treatment success depends heavily on patient compliance, and complex cases may require additional refinements, prolonged treatment, auxiliary appliances, and potentially higher costs. This review critically evaluates the benefits, clinical challenges, and limitations of clear aligners in orthodontic–orthognathic treatment. It highlights the importance of careful case selection, realistic assessment of biomechanical predictability, and coordinated orthodontic and surgical planning to achieve stable functional and aesthetic outcomes.