Study Objectives: While insomnia and migraine are often comorbid, the shared and distinct neuroanatomical substrates underlying these disorders and the brain structures associated with the comorbidity are unknown. We aimed to identify patterns of neuroanatomical substrate alterations associated with migraine and insomnia comorbidity. Methods: High-resolution T1-weighted images were acquired from subjects with insomnia, migraine, and comorbid migraine and insomnia, respectively, and healthy controls (HC). Direct group comparisons with HC followed by conjunction analyses identified shared regional gray matter volume (GMV) alterations between the disorders. To further examine large-scale anatomical network changes, a seed-based structural covariance network (SCN) analysis was applied. Conjunction analyses also identified common SCN alterations in two disease groups, and we further evaluated these shared regional and global neuroanatomical signatures in the comorbid group. Results: Compared with controls, patients with migraine and insomnia showed GMV changes in the cerebellum and the lingual, precentral, and postcentral gyri (PCG). The bilateral PCG were common GMV alteration sites in both groups, with decreased structural covariance integrity observed in the cerebellum. In patients with comorbid migraine and insomnia, shared regional GMV and global SCN changes were consistently observed. The GMV of the right PCG also correlated with sleep quality in these patients. Conclusion: These findings highlight the specific role of the PCG in the shared pathophysiology of insomnia and migraine from a regional and global brain network perspective. These multilevel neuroanatomical changes could be used as potential image markers to decipher the comorbidity of the two disorders.