<p>The study aimed to analyze the alterations of cortical thickness (CT) in comorbidity of insomnia and sleep apnea (COMISA) patients of varying severity and the relationships of these CT changes with clinical measures. The study included 34 COMISA patients and 24 healthy controls (HCs). The patients received structural MRI as well as measures associated with respiration, sleep, cognition, and mood, and were classified as mild and moderate (MC) or severe (SC) groups. The CT for COMISA was analyzed through surface-based morphometry (SBM). Voxel-wise differences in CT between two groups were analyzed. Individual CT maps of MC, SC, and HC groups were used in analysis of variance for investigating how COMISA severity at various stages affects CT. Partial correlation analysis was used for analyzing the relations between changes in CT and clinical measures. Reduced CT was located in four clusters, including left supramarginal gyrus, left precentral and postcentral gyri, right pericalcarine and lingual gyri, and right rostral and caudal middle frontal gyri in COMISA group. The CT of left supramarginal gyrus was found in MC group, whereas all four clusters in SC group Moreover, the partial correlation analysis results revealed that CT was significantly related to respiration measures (AHI and LSaO₂). In conclusion, our findings showed a greater cortical thinning with increasing OSA severity within the COMISA cohort, which was negatively correlated with respiration measures, suggesting that respiratory impairment (e.g., intermittent hypoxia) may contribute to the neuroanatomical alterations in these patients.</p>