A cross section processing method and a cross section processing apparatus are provided in which it is possible to form a flat cross section in a sample composed of a plurality of substances having different hardness by a focused ion beam. The etching of a processing area is performed while variably controlling the irradiation interval, the irradiation time, or the like of a focused ion beam based on cross section information of an SEM image obtained by the observation of a cross section. In this way, even if a sample is composed of a plurality of substances having different hardness, it is possible to form a flat observation surface with a uniform etching rate.