Objective This study aimed to elucidate the key factors contributing to enamel demineralization in or-thodontic patients, identify biomarkers associated with its occurrence, and explore the relationship between enamel demine-ralization and oral microbiota in adolescent orthodontic patients. Methods Two groups of patients were selec-ted, one group with self-ligating brackets (Group S) and the other with traditional metal brackets (Group M), with 22 participants in each group. Subgingival plaque was collected for microbiome analysis at the baseline of orthodontic treatment and after 3 months. Simultaneously, saliva was collected to measure the levels of secretory immunoglobulin A (sIgA). Clinical indices such as the enamel demineralization index, plaque index (PLI), gingival index, and periodontal index were statistically analyzed during monthly recall visits. Results After 3 months of orthodontic treatment, the incidence of enamel demineralization among patients significantly increased, with an average increase of over 20% in demineralization rates. In Group S, the abundance of Fusobacterium, Campylobacter, Neisseria, and Prevotella significantly increased after 3 months of orthodontics (P<0.05). In Group M, the abundance of Rothia significantly increased (P<0.05). The abundance of Arthrobacter, Bacillus, Acinetobacter, Prevotella, and Campylobacter was positively correlated with enamel demineralization and PLI scores. The levels of sIgA in saliva were negatively correlated with the occurrence of enamel demineralization, with a significant decrease in sIgA levels in Group S after orthodontic treatment (P<0.01). Conclusion Orthodontic patients with self-ligating brackets are more prone to enamel demineralization, and Campylobacter and Prevotella may be key bacterial species that exacerbate enamel demineralization in adolescent orthodontic patients. A decrease in salivary sIgA levels may indicate an increased risk of enamel demineralization in or-thodontic patients.