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Objective This study aimed to analyze the status of hypoxia in non-rapid eye movement (NREM) sleep in children with otitis media with effusion (OME). Methods A total of 232 children with OME and/or adenotonsillar hypertrophy were enrolled in this retrospective study between August 2020 and November 2021. Polysomnographic monitoring was carried out, and the differences in polysomnographic results between the experimental group (children with OME and adenotonsillar hypertrophy) and control group (children with adenotonsillar hypertrophy only) were compared. Results The lowest oxygen saturation level during sleep was significantly lower in the experimental group (n  =  36) than in the control group (n = 196). However, the apnea-hypopnea index, respiratory disorder index, apnea index, obstructive apnea index, obstructive apnea-hypopnea index, and mixed apnea-hypopnea index were significantly higher in the experimental group than in the control group. More importantly, the apnea-hypopnea index, the oxygen desaturation index, oxygen desaturation events, the average heart rate during NREM sleep, and the NREM stage in total sleep time were also significantly higher in the experimental group than in the control group. Conclusions Hypoxia during NREM sleep may affect the severity of OME in children.