A method of manufacturing an analytical sample by a secondary ion mass spectrometry method is provided, which comprises a step of forming a separation layer over a substrate, a step of forming one of a thin film and a thin-film stack body to be analyzed over the separation layer, a step of forming an opening portion in one of the thin film and the thin-film stack body, a step of attaching a supporting body to one of a surface of the thin film and a surface of a top layer of the thin-film stack body, and a step of separating one of the thin film and the thin-film stack body from the substrate.