An object of the present invention is to provide a method for conveniently analyzing sugar chain (isomer) structure using a sample of approximately 1 picomole, which is generally subjected to analysis in proteomics without using any sugar chain preparation. The present invention relates to a method for analyzing sugar chain structure, comprising a step of obtaining the fragmentation pattern of a test sugar chain through fragmentation of the test sugar chain and a step of predicting the structure of the test sugar chain through comparison of the sugar chain predicted fragmentation pattern data generated based on fragmentation pattern templates with the fragmentation pattern of the test sugar chain.