This study aimed to explore the effects of chronic intermittent hypoxia (CIH) on learning, memory, and hippocampal miRNA expression profiles in rats. Sixty male Sprague-Dawley rats were randomly divided into four groups: control, intermittent hypoxia for 1 week (IH1W), 2 weeks (IH2W), and 4 weeks (CIH4W). The rats underwent hypoxia/reoxygenation cycles, and the Morris water maze test was used to evaluate learning and memory abilities. High-throughput sequencing and qPCR were employed to analyze changes in miRNA expression in the hippocampus. The study found that differentially expressed miRNAs (DE-miRNAs) may be involved in cognitive dysfunction under CIH conditions by regulating predicted target gene signaling pathways, such as metabolic pathways, MAPK pathway, axon guidance, ubiquitination, and apoptosis. This study revealed the roles and mechanisms of key miRNAs in CIH-induced cognitive dysfunction, highlighting the critical role of miRNAs in regulating target gene expression, thereby contributing to the pathogenesis of cognitive impairment associated with obstructive sleep apnea syndrome (OSAS). These findings provide important molecular insights and potential therapeutic targets for further research on OSAS-related cognitive impairment.