A cross-section processing and observation method performed by a cross-section processing and observation apparatus comprises a cross-section processing step of forming a cross-section by irradiating a sample with an ion beam; a cross-section observation step of obtaining an observation image of the cross-section by irradiating the cross-section with an electron beam; and repeating the cross-section processing step and the cross-section observation step so as to obtain observation images of a plurality of cross-sections. In a case where Energy Dispersive X-ray Spectrometry (EDS) measurement of the cross-section is performed and an X-ray of a specified material or of a non-specified material that is different from a pre-specified material is detected, an irradiation condition of the ion beam is changed so as to obtain observation images of a plurality of cross-sections of the specified material, and the cross-section processing and observation of the specified material is performed.