Neurological paroxysmal disease is a large group of clinical syndrome with a characteristic of sudden, recurrent, self-limiting. Clinically, routine biochemical or imaging examinations are usually with no significant abnormalities in the interictal period. However, magnetoencephalography (MEG), as an important electrophysiological tool in studying brain magnetic signals and monitoring brain electric activity, has highly temporal and spatial resolution for its noninvasive measurement of human brain with superconducting quantum interference. Therefore, it has been gradually used in researching for functional activities and mechanisms of the neuropsychiatric disorders and the advanced brain activity. There mainly reviewed the application and studies of MEG in epilepsy, paroxysmal kinesigenic dyskinesias and migraine.