Objective To analyze the effect of metal self-ligating brackets on periodontal microenvironment indicators in patients with malocclusion. Methods A total of 80 patients with malocclusion admitted to Huanghua Hospital of Traditional Chinese Medicine from June 2023 to July 2025 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 conventional straight wire brackets, and the observation group was treated with metal self-ligating brackets. Both groups adopted the same sequence of arch wires and force application protocols, and received consistent oral hygiene instructions. The orthodontic effect, periodontal microenvironment indicators and inflammatory factor levels in gingival crevicular fluid were compared between the two groups. Results The scores of tooth alignment and occlusal relationship improvement in the observation group were lower than those in the control group (P <0.05). The plaque index and gingival index in the observation group were lower than those in the control group (P <0.05). The levels of IL-6, TNF-α and IL-1β in gingival crevicular fluid of the observation group were lower than those of the control group (P <0.05). Conclusion Compared with conventional straight wire brackets, metal self-ligating brackets can more effectively improve tooth alignment and occlusal relationship in patients with malocclusion. During treatment, they are more conducive to maintaining periodontal health, alleviating periodontal inflammatory response and balancing the flora in the periodontal microenvironment.