The present invention relates to an electron microscope plasma cleaner for cleaning an electron microscope by using plasma, the cleaner including a vacuum chamber in which the sample is disposed; an electron gun for producing the electron beam and outputting the produced electron beam to the sample; an electron lens for magnifying the electron beam transmitting the sample and projecting the electron beam onto a fluorescent screen; a radio frequency controller for producing a first signal having radio frequency within a given range; and a plasma head for producing the plasma, receiving the first signal from the radio frequency controller, producing activated oxygen radicals and ions by using the plasma and the first signal, and supplying the activated oxygen radicals and ions to the interior of the vacuum chamber.