Provided is a cross-section processing observation method capable of easily and accurately forming a cross-section used to observe a sample's inside, and a cross-section processing observation apparatus for cross-section processing. The method includes a design data acquisition step acquiring design data of a three-dimensional structure of a sample having three-dimensional structure, a moving step moving the sample based on coordinate information of the design data, a surface observation step acquiring an observation image of a surface of the sample, a cross-section forming step irradiating the sample's surface with an ion beam to form a cross-section of the three-dimensional structure, a cross-section observation step acquiring an observation image of the sample's cross-section, and a display step displaying image data, among pieces of the design data, of surface and cross section corresponding to respective locations of the surface and the cross section.