Multi-bracket appliances have long been established as tools for treating malocclusions. However, the complex construction and difficulty in cleaning due to their long-term intraoral retention have hindered the prevention of caries and periodontitis. In this study, professional mechanical tooth cleaning (PMTC), including tooth-brushing instructions, was continuously performed for 3 months in 24 patients who had worn multi-bracket appliances for more than 6 months, and changes in the oral and gut microbiota were examined using one-way repeated-measures analysis of variance. Additionally, changes in bacterial flora associated with different treatment durations were verified using the Pearson correlation coefficient. The results showed that continuous PMTC significantly reduced the amount of plaque in the oral cavity. No significant changes were observed in the oral or gut microbiota and no significant increase in pathogenic bacteria was observed. Therefore, our results suggest that continuous PMTC during orthodontic treatment with multi-brackets may inhibit the growth of pathogenic bacteria by maintaining a clean oral environment and avoiding dysbiosis in both the oral and gut microbiota. Significant changes in the gut microbiota with different treatment durations suggested that differences in food intake and food choices at each treatment stage of orthodontic treatment may affect the gut microbiota.