Extrusion of anterior teeth is a common manifestation of periodontitis. Orthodontic intrusion is an effective approach for improving occlusion and periodontal health. This study aimed to identify the optimal protocols for maxillary incisor intrusion using clear aligner (CA) in patients with periodontitis. A validated finite element model was established, including the CA, teeth, periodontal ligaments (PDLs), and alveolar bone with three levels of bone height (simulating mild to severe periodonti