Objective We aimed to investigate the difference between the bacterial profiles of the nasal cavities and adenoid surfaces of children with chronic rhinosinusitis (CRS). We also intended to determine and analyze the potential correlation between the pre- and post-adenoidectomy differences in the nasal bacterial profile and clinical prognosis. Methods The clinical information of pediatric patients was collected. All the children underwent adenoidectomy (with or without tonsillectomy), and swab samples were collected during the operation. Visual analog scales (VAS) were used at 3, 6, and 12 months postoperatively. At the 12-month follow-up examination, swab samples were collected again. PCR amplification was performed of the v3-v4 variable regions of 16S rRNA of the collected specimens, as well as high-throughput sequencing using the Illumina platform. The species information was obtained by OTUs clustering, species annotation, and α-diversity analysis. Results Twenty-two male and eight female pediatric patients were included in the investigation The most abundant genus level bacterial representatives on the nasal surface before adenoidectomy were Moraxella catarrh, Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus, whereas on the surface of adenoids, they were Streptococcus pneumonia, Haemophilus influenza, Nucleobacter, and Moraxella catarrhalis. One year postoperatively, the bacteria with the highest abundance on the nasal surface at the genus level were Moraxella catarrhalis, Streptococcus pneumonia, Staphylococcus aureus, and non-culturable Dolosigranulum. One year postoperatively, the bacterial richness in the nasal cavity was significantly higher than at baseline ( P < .05). Furthermore, the subjective nasal score of all children significantly decreased at 3, 6, and 12 months postoperatively ( P < .01). Conclusion The preoperative bacterial abundance of the nasal cavity and the adenoid surfaces was similar, showing a clear correlation. No single specific bacterium was established to be a dominant species associated with the development of CRS in children. The post-adenoidectomy bacterial richness in the nasal cavity was significantly increased, which may be closely related to the relief of postoperative sinusitis symptoms.