Previous studies demonstrated that there was abnormal functional connectivity (FC) in the amygdala subregions in obstructive sleep apnea (OSA), which was associated with cognitive function. However, it is not clear whether these abnormalities can be improved after continuous positive airway pressure (CPAP) treatment. Therefore, the aim of this research was to investigate the changes in FC of amygdala subregions with other brain regions after 6 months of CPAP treatment (post-CPAP) in patients with OSA.Fifteen OSA patients underwent Magnetic Resonance Imaging prior to CPAP treatment (pre-CPAP) and following CPAP treatment. The amygdala was divided into six subregions, including bilateral dorsal amygdala (DA), medial amygdala (MA) and ventral amygdala (VA). The FC was calculated by using the amygdala subregions as seeds. A paired sample T-test was employed to assess alterations in the amygdala subregions FC of pre-CPAP and post-CPAP OSA patients, and correlation analysis was then conducted to evaluate the association between the changed FC and clinical assessment.Compared to pre-CPAP OSA patients, post-CPAP OSA patients displayed an enhanced FC between the left DA and the right posterior cingulate cortex (PCC), whereas the FC between the left MA and the right postcentral gyrus, and between the right MA and the left middle frontal gyrus, decreased. Moreover, significant correlation between the FC value of left DA-right PCC and Hamilton Anxiety Inventory scores was found in pre-CPAP OSA patients.Altered FC between the amygdala subregions and other brain regions in OSA patients induced by CPAP treatment was related to cognitive, emotional, and sensorimotor function. Our study found altered FC between amygdala subregions and cognitive and motor-related brain regions in post-CPAP OSA patients, providing potential neuroimaging indicators for CPAP treatment.