Previous studies have shown that the structural and functional impairments of hippocampal subregions in patients with obstructive sleep apnea (OSA) are related to cognitive impairment. Continuous positive airway pressure (CPAP) treatment can improve the clinical symptoms of OSA. Therefore, this study aimed to investigate functional connectivity (FC) changes in hippocampal subregions of patients with OSA after six months of CPAP treatment (post-CPAP) and its relationship with neurocognitive function. We collected and analyzed baseline (pre-CPAP) and post-CPAP data from 20 patients with OSA, including sleep monitoring, clinical evaluation, and resting-state functional magnetic resonance imaging. The results showed that compared with pre-CPAP OSA patients, the FC between the right anterior hippocampal gyrus and multiple brain regions, and between the left anterior hippocampal gyrus and posterior central gyrus were reduced in post-CPAP OSA patients. By contrast, the FC between the left middle hippocampus and the left precentral gyrus was increased. The changes in FC in these brain regions were closely related to cognitive dysfunction. Therefore, our findings suggest that CPAP treatment can effectively change the FC patterns of hippocampal subregions in patients with OSA, facilitating a better understanding of the neural mechanisms of cognitive function improvement, and emphasizing the importance of early diagnosis and timely treatment of OSA.