Obstructive sleep apnea (OSA) is a chronic, multisystem sleep disorder that has been linked with dementia, stroke and increased risks of cardiovascular disease. Continuous positive airway pressure (CPAP) is the most common treatment method for OSA patients, but its effect on different organ systems and to reverse the rate of cognitive decline is still unclear. In this study, we evaluated neurochemical changes of untreated and CPAP treated OSA patients versus healthy controls in twelve brain regions using a semi-laser based accelerated five-dimensional (5D) echo-planar J-resolved spectroscopic imaging (EP-JRESI) sequence. We also explored the relationship between brain metabolite ratios and apnea hypopnea index (AHI), a measure indicative of the severity of sleep apnea. We observed significant differences of several metabolites in many brain regions. We also found that, among other metabolites, AHI correlated positively with lactate in right parietal insular cortex. This may be the result of hypoxemia and tissue hypoxia during sleep caused by OSA. To validate our findings, further longitudinal studies using a large cohort of OSA subjects before and after CPAP are required.