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The aim of this study was to investigate the changes in insular cortex metabolites and the correlation with clinical manifestations in patients with obstructive sleep apnea syndrome (OSA). Lateral insular metabolite levels were measured and relevant ratios were calculated in OSA patients and healthy individuals, including N-acetyl aspartate/creatine (NAA/Cr), choline/creatine (Cho/Cr), inositol/creatine (Ins/Cr), glutamate compound/creatine (Glx/Cr), N-acetyl aspartate/choline (NAA/Cho), and lactic acid (Lac). Participants’ scores on the Hamilton Anxiety Scale (HAMA), the Hamilton Depression Scale (HAMD), the Pittsburgh Sleep Quality Index (PSQI), and the Epworth Sleepiness Scale (ESS) were also evaluated. Apnea–Hypopnea Index, the lowest arterial oxygen saturation, and the mean arterial oxygen saturation (MSaO2) values were monitored by polysomnography. NAA/Cr, Glx/Cr, and NAA/Cho values in the insular cortex were significantly decreased, whereas HAMA, HAMD, PSQI, and ESS scores were significantly higher in OSA patients compared with the control participants. HAMA and HAMD scores showed a significant negative correlation with the NAA/Cho value in the insular cortex and a positive correlation with PSQI and ESS scores. PSQI scores were correlated positively with the Cho/Cr and Ins/Cr ratios in the left insular cortex, but correlated negatively with the NAA/Cho ratio. The symptoms of anxiety and depression in OSA patients may be associated with insular neuron damage or dysfunction; proton magnetic resonance spectroscopy can provide an objective imaging basis for the early diagnosis and treatment of OSA in clinical practice.