Objective To analyze the effect of orthodontic micro-implantation on root resorption, masticatory function and stability in patients with skeletal class Ⅱ malocclusion of thin-gingiva type and thick-gingiva type. Methods A total of 152 patients with skeletal class Ⅱ malocclusion admitted to the Department of Stomatology, the 960th Hospital of the PLA from March 2023 to March 2024 were selected as the research subjects. According to different periodontal phenotypes, they were divided into thin-gingiva type group and thick-gingiva type group, with 76 patients in each group. Both groups were treated with orthodontic micro-implantation. The periodontal health indexes, root resorption, masticatory function and stability were compared between the two groups. Results After treatment, the levels of PD and PLI in the thick-gingiva type group were lower than those in the thin-gingiva type group (P<0.05 ). After treatment, the volume values of maxillary and mandibular canines, lateral incisors and central incisors in the thick-gingiva type group were higher than those in the thin-gingiva type group (P<0.05). After treatment, the occlusal force and masticatory efficiency in the thick-gingiva type group were higher than those in the thin-gingiva type group (P<0.05). The incidence of peri-implantitis in the thick-gingiva type group (3.95%) was lower than that in the thin-gingiva type group (14.47%), and the success rate of implantation (90.79%) was higher than that in the thin-gingiva type group (78.95%) (P<0.05). Conclusion Compared with patients with skeletal class Ⅱ malocclusion of thingingiva type, patients with skeletal class Ⅱ malocclusion of thick-gingiva type have a healthier periodontal microenvironment, less root resorption, better masticatory function and stability after orthodontic micro-implantation treatment. It is worthy of clinical application.