A cross section processing method to be performed on a sample by irradiating the sample having a layer or a structure of an organic substance on a surface at a cross section processing position thereof with a focused ion beam using a focused ion beam apparatus includes: a protective film forming step for forming a protective film on the surface of the layer or the structure of the organic substance by irradiating the surface of the sample including the cross section processing position with the focused ion beam under the existence of source gas as the protective film; and a cross section processing step for performing cross section processing by irradiating the cross section processing position formed with the protective film with the focused ion beam at a voltage higher than an accelerating voltage in the protective film forming step.