A method for identifying the binding site of a biomolecule and a low-molecular-weight compound, comprising the following steps of mixing the low-molecular-weight compound with the biomolecule under acellular conditions to obtain a biomolecule bound to the low-molecular-weight compound, fragmenting the biomolecule bound to the low-molecular-weight compound, and fractionating the fragment, thereby preparing fractionated fragments (fractions) of the biomolecule bound to the low-molecular-weight compound, wherein the biomolecule is fragmented by an enzyme selected from the group consisting of protease, peptidase, nuclease, glycolytic enzyme, and lipase, or chemical degradation, and wherein fractionation is performed by liquid chromatography or capillary electrophoresis, and then subjecting a fractionated fragments of the biomolecule bound to the low-molecular-weight compound to Raman spectroscopy and detecting a fraction having a Raman peak derived from the low-molecular-weight compound bound to a fragment of the biomolecule, and then subjecting all or some fractions subjected to Raman spectroscopy to mass spectrometry, wherein, among said all or some of the fractions subjected to Raman spectroscopy, a fraction having a Raman peak derived from the low-molecular-weight compound bound to a fragment of the biomolecule as detected via said Raman spectroscopy is subjected to the mass spectrometry, whereby the binding site of the low-molecular-weight compound within the biomolecule is identified by detecting a fraction having a Raman peak derived from the low-molecular-weight compound bound to a fragment of the biomolecule via Raman spectroscopy, obtaining the mass spectrometric results for a fraction having a Raman peak derived from the low-molecular-weight compound, and comparing the results with the mass information of the biomolecule, wherein the low-molecular-weight compound exhibits a Raman peak distinguishable from that of the biomolecule. mixing the low-molecular-weight compound with the biomolecule under acellular conditions to obtain a biomolecule bound to the low-molecular-weight compound, fragmenting the biomolecule bound to the low-molecular-weight compound, and fractionating the fragment, thereby preparing fractionated fragments (fractions) of the biomolecule bound to the low-molecular-weight compound, wherein the biomolecule is fragmented by an enzyme selected from the group consisting of protease, peptidase, nuclease, glycolytic enzyme, and lipase, or chemical degradation, and wherein fractionation is performed by liquid chromatography or capillary electrophoresis, and then subjecting a fractionated fragments of the biomolecule bound to the low-molecular-weight compound to Raman spectroscopy and detecting a fraction having a Raman peak derived from the low-molecular-weight compound bound to a fragment of the biomolecule, and then subjecting all or some fractions subjected to Raman spectroscopy to mass spectrometry, wherein, among said all or some of the fractions subjected to Raman spectroscopy, a fraction having a Raman peak derived from the low-molecular-weight compound bound to a fragment of the biomolecule as detected via said Raman spectroscopy is subjected to the mass spectrometry,