Objective To explore the effect of micro-implant anchorage on occlusal force and masticatory efficiency in the treatment of skeletal class Ⅱ malocclusion. Methods A total of 80 patients with skeletal class Ⅱ malocclusion admitted to our hospital from March 2023 to March 2024 were selected, and they were divided into the control group and the observation group by the random number table method, with 40 patients in each group. The control group was treated with headgear J-hook orthodontics, and the observation group was treated with micro-implant anchorage. The orthodontics effect, masticatory function and adverse reactions were compared between the two groups. Results After correction, the SNB, ANB, U1-SN, L1-MP, OJ, OB, U6A-RL, U6S-RL, UL-Y and NLA in the observation group were better than those in the control group (P <0.05). There was no statistically significant difference in SNA between the two groups after correction (P >0.05). The occlusal force and masticatory efficiency in the observation group after correction were higher than those in the control group (P <0.05). The incidence of adverse reactions in the observation group (5.00%) was lower than that in the control group (22.50%) (P <0.05). Conclusion Micro-implant anchorage has a definite therapeutic effect in the treatment of skeletal class Ⅱ malocclusion. It can effectively improve the orthodontics status, enhance masticatory function, and reduce adverse reactions.