Background: Temporary anchorage devices (TADs) are maximum anchorages that have been widely used in orthodontic treatment. Poor oral hygiene might result in inflammation and decreased stability of the TADs. In this study, we aimed to unveil the differences in the microbiome between TADs under different oral hygiene conditions.Methods: Oral hygiene condition was stratified by Oral Hygiene Index- Simplified (OHI-S), Plaque Index (PLI), and Gingival Inflammation. Scanning electron microscopy (SEM) was used to analyze the existence of biofilm on the surface of 8 TADs, Ten TADs from the good oral hygiene group (GOH), and 10 TADs from the poor oral hygiene group (POH) were analyzed by 16S rRNA gene sequencing. Results: Principal coordinate analysis (PCoA) based on β diversity revealed differential sample clusters depending on oral hygiene conditions. When comparing specific genera, Veillonella, Streptococcus, Neisseria, were more enriched in the poor oral hygiene group. Conversely, Fusobacterium, Porphyromonas exhibited more richness in the good oral hygiene group. TADs in the good oral hygiene group demonstrated enriched microbial activities involved with signal transduction, cell mobility and energy metabolism. TADs in poor oral hygiene demonstrated enriched functions in membrane transport, transcription and signaling molecules and interactions. Conclusions: In summary, this analysis elucidated the difference in total composition and function of TADs oral microorganisms between patients with good oral hygiene and patients with poor oral hygiene, which highlighted the importance of maintaining good oral hygiene in TADs treatment.