One mode is a method for the structural analysis of an organic compound by MALDI mass spectrometry, including: a sample preparation process (S1) which includes preparing a sample by mixing a specimen containing an organic compound to be analyzed with a predetermined matrix at a mixture ratio within a range from 1:5 to 1:5000 in molar ratio; a mass spectrometry process (S3) which includes irradiating the prepared sample with a laser beam having a spot size equal to or smaller than 15 μm to generate ions originating from a component of the specimen in the sample, and performing a mass spectrometric analysis of the generated ions; and an analyzing process (S4) which includes detecting, from a mass spectrum acquired in the mass spectrometry process, ions including product ions resulting from in-source decay, and estimating the structure of the organic compound to be analyzed based on information concerning the ions.