Migraine is a complicated neurological disability disease and still not been clarified. PFO may be a subset to cause migraine. Therefore, this study aims to analysis the value of PFO in grey matter and white matter lesions of migraine. We found that the changes mainly in frontal cortex, precentral gyrus regions of pain modulating area between patients with PFO and without PFO in migraine. However, out results do not support the relationship between PFO and white matter lesions. This findings may provide a new insight for clinical treat strategy.