Objective To investigate the biomechanical characteristics of orthodontic tooth movement at different alveolar bone heights and provide a theoretical reference for orthodontic clinical treatment. Methods Four groups of mandibular dentition finite element models were established: the normal alveolar bone height, and 1/3, 1/2, and 2/3 reductions in height. The lingual, distal, and intrusion movements of the mandibular central incisor were simulated under different loads. The distribution and variations in periodontal stress and tooth displacement were analyzed. Results Under three movements, the degree of stress concentration in the cervical area of the tooth and the periodontal equivalent force increased as the alveolar bone height decreased and the orthodontic force increased. Meanwhile, the displacement at each observation point and the crown–root displacement difference increased, and the tendency for inclination movement of the teeth aggravated. When the alveolar bone height was reduced to 2/3, the orthodontic force under lingual and distal movement increased to 150 g and that under intrusion movement increased to 100 g. The periodontal equivalent force increased to the maximum value, and the tendency of tooth inclination movement was most significant. Conclusions A reduction in the alveolar bone height aggravates the stress concentration at the top of the alveolar ridge and the tendency for inclination movement of the teeth. For orthodontic patients with an inferior periodontal condition, the orthodontic force should be reduced according to the alveolar bone height to ensure a safe and effective orthodontic treatment.