The present invention provides a three-dimensional structure analysis method that extracts monosaccharide bonding patterns significant for elucidation of the formation of the three-dimensional structures of polysaccharides when the alignments of local structures are given for those polysaccharides. This three-dimensional structure analysis method comprises inputting the alignment of the local structures of a polysaccharide; inputting coordinate data relating to polysaccharides to which each local structure belongs; detecting interactions between substituents of each hydroxyl group within a local structure and hydroxyl groups that serve as acceptors of other monosaccharides; evaluating the interaction patterns; and outputting information relating to the interactions.