The object of the present invention is to analyze a functional organic compound with high accuracy. In the present invention, cluster ions are accelerated so that the kinetic energy of cluster ions is less than 3.1 eV per one atom that makes up the cluster ion and the cluster ions enter a sample. Since the functional organic compound in the sample is etched without the breakdown of the chemical structure, the functional organic compound, which has not been chemically denatured, is exposed on the surface of the sample. By alternately performing the etching and the surface analysis of the sample, or performing the surface analysis of the sample while performing the etching, the sample can be accurately analyzed in the depth direction.