Objective To investigate the characteristics of microbial diversity in the tonsil and adenoid tissues of children with sleep-disordered breathing (SDB). Methods This study enrolled six pediatric patients diagnosed with SDB via polysomnography between August 2024 and September 2025. All patients underwent tonsillectomy and adenoidectomy at the Department of Otolaryngology, Jingzhou Central Hospital. Tonsil and adenoid tissues from the same patient were collected during surgery and subjected to metagenomic sequencing. The Shannon diversity index curve, relative abundance, and microbial distribution in the tonsil and adenoid tissues of the 6 patients were analyzed and compared. Results The analysis of the Goods_Coverage value indicated that the sequencing depth of the samples was reasonable. The Shannon and Simpson indices confirmed that all samples had a high level of species diversity. The Alpha diversity assessment showed that the species richness of the adenoid tissue samples (ACE/Chao1) was significantly higher than that of the tonsil tissue samples. The comparison of microbial analysis of the tonsil and adenoid tissues from the 6 children revealed that the local microecological structure of the adenoid group was highly stable and highly homogeneous within the group; the individual heterogeneity within the tonsil group was prominent, and the community complexity and species diversity were higher, with the presence of cross-border microorganisms such as viruses and fungi. Proteobacteria and Firmicutes constituted the predominant phyla in both groups, whereas significant discrepancies were observed in their relative abundance profiles. Conclusions This study using metagenomic sequencing reveals that the dominant bacterial species in the paired tonsil and adenoid tissues from the same patient are highly similar. The microecosystem of adenoid tissues exhibits robust stability and excellent intra-group homogeneity, whereas the corresponding tonsil tissues presents significant microecological dysbiosis and individual heterogeneity. Recurrent chronic inflammation may disrupt the local microecological homeostasis of the tonsils.