Objective Migraine is a complex brain dysfunction disease with a prevalence of 14.4% worldwide. Functional connectivity measures the statistical interdependences between two neural signals, and different functional connectivity patterns reflect different models of how brain regions work together. Therefore, investigating functional connectivity between different brain regions is important for understanding the pathophysiological mechanisms of migraine. Previous electroencephalogram-based functional connectivity analyses in migraine patients have mainly focused on visual and painful stimulation. We sought to investigate cortical responses to somatosensory stimulation in migraine patients during the interictal period, with the aims of better understanding the neurological dysfunction in migraine and providing clues for the prevention and treatment of migraine.Methods Twenty-three patients with migraine without aura, 10 patients with migraine with aura, and 28 healthy controls were recruited. Detailed basic data and medical history were collected from all participants, and the scale assessment was completed. All participants underwent electroencephalogram recording under median nerve somatosensory stimulation. The coherence of 68 brain regions was calculated as functional connectivity and correlations with clinical parameters were evaluated.Results Functional connectivity in migraine without aura and migraine with aura patients is atypical compared to controls under median nerve somatosensory stimulation, and the abnormal functional connectivity mainly involves areas of sensory discrimination, pain modulation, emotional cognition, and visual processing. The cerebral cortex in migraine without aura and migraine with aura patients may possess a common way of responding to somatosensory stimulation. The functional connectivity abnormalities in migraine patients have correlations with clinical features and may partly reflect the severity of migraine.Conclusion Our results provide evidence of altered functional connectivity in migraine patients under somatosensory stimulation, and suggest that the dysfunction in the brain network may be involved in the pathological process of migraine.