Before progress was recently made in the application of temporary anchorage devices (TADs) in bio-mechanical design, orthodontists were rarely able to intrude molars to reduce upper posterior dental height (UPDH). However, TADs are now widely used to intrude molars to flatten the occlusal plane or induce counterclockwise rotation of the mandible. Previous studies involving clinical or animal histological evaluation on changes in periodontal conditions after molar intrusion have been reported, however, studies involving human histology are scarce. This case was a Class I malocclusion with a high mandibular plane angle. Upper molar intrusion with TADs was performed to reduce UPDH, which led to counterclockwise rotation of the mandible. After 5 months of upper molar intrusion, shortened clinical crowns were noticed, which caused difficulties in oral hygiene and hindered orthodontic tooth movement. The mid-treatment cone-beam computed tomography revealed redundant bone physically interfering with buccal attachment and osseous resective surgeries were followed. During the surgeries, bilateral mini screws were removed and bulging alveolar bone and gingiva were harvested for biopsy. Histological examination revealed bacterial colonies at the bottom of the sulcus. Infiltration of chronic inflammatory cells underneath the non-keratinized sulcular epithelium was noted, with abundant capillaries being filled with red blood cells. Proximal alveolar bone facing the bottom of the gingival sulcus exhibited active bone remodeling and woven bone formation with plump osteocytes in the lacunae. On the other hand, buccal alveolar bone exhibited lamination, indicating slow bone turnover in the lateral region.