Magnetic resonance imaging (MRI) studies have demonstrated anatomical and functional alterations of brain regions in patients with migraine, and the efficacy of acupuncture for migraine could regulate these abnormal alterations. However, its pathogenesis remains ambiguous, and inconsistent results have been reported. The purpose of this study was to explore abnormal structural and functional alterations in patients with migraine using voxel-based morphometry (VBM) analysis and a seed-based functional connectivity (FC) approach and to provide a basis for future research.