Growing evidence suggests that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can affect the central nervous system (CNS), and insomnia-related acute and long-term CNS sequelae may be suffered by infected patients. Nevertheless, as a common sub-typic strain of SARS-CoV-2, it is currently unknown the impacts of Omicron comorbid with insomnia on brain cortex. The purpose of this study was to mine the neural markers involving cortical grey matter volume (GMV), thickness, and surface area within Omicron individuals either with or without insomnia. Additionally, correlations between these morphological metrics and neuropsychiatric assessments were analyzed. 234 participants were recruited from a prospective cross-sectional study cohort during the Omicron pandemic (December 2022-May 2023) at the Second Xiangya Hospital (China). We further divided participants into healthy controls (HCs), Omicron infection with insomnia group (Omicron_insomnia group), and Omicron infection without insomnia group (Omicron_non_insomnia group). Based on T1-weighted MPRAGE image, cortical thickness, surface area, and GMV were compared via surface-based morphometry (SBM) analysis, and significant morphological metrics were then correlated with neuropsychiatric manifestations. Our findings revealed altered cortical morphology in Omicron individuals. Morphological changes in the temporal, frontal, cingulate, transverse collateral, and lingual gyrus were independent from insomnia comorbidity. The decreased cortical thickness in superior temporal gyrus (STG) was a specific feature for Omicron infection comorbid with insomnia. Then, we discovered greater morphological size indicating neuropsychiatric improvement. This study explores the neural mechanisms underlying Omicron infection comorbid with insomnia, which will help to promote improvement in post-Omicron neuropsychiatric prognosis and clinical management.