Introduction: Patients with severe periodontitis typically present with pathologic tooth migration. To improve esthetics and masticatory function, orthodontic treatment is required. Research on periodontal orthodontic treatment has been sparse, particularly from the microbial perspective. Hence, we analyzed the microbial and clinical changes in patients with well-controlled periodontitis in the early stage of orthodontic treatment. Methods: Ten patients with well-controlled periodontitis were asked to collect saliva before and 1 and 3 months after appliance placement (T0, T1, and T2, respectively) and underwent clinical examinations before and 1, 3, and 6 months after appliance placement (T0, T1, T2, and T3, respectively). The microbial community of saliva was analyzed by 16S rRNA gene sequencing. Gingival index, the plaque index, and the probing pocket depth were clinically assessed. Results: The plaque index significantly increased from T0 to T1 and decreased at T2 and T3. The probing pocket depth and gingival index increased slightly at T2, but not significantly, in both the high-risk site and low-risk site. The alpha and beta diversity increased at T1. The microbial community structure was similar at T0 and T2. The relative abundance of core genera and periodontal pathogens was stable during the initial 3 months of orthodontic treatment. Conclusions: The orthodontic appliance promoted plaque accumulation and altered the microbial community of patients with well-controlled periodontitis during the first month of orthodontic treatment. The microbial community returned to the basal composition at 3 months after appliance placement, and the periodontal inflammation during the 6-months orthodontic treatment was under control.