The invention relates to an N-saccharide structure base construction method and system based on regular expressions. The method comprises the steps that each monosaccharide in a pentasaccharide core is used as a node, and all the nodes are numbered to clarify a monosaccharide category represented by the nodes; according to the connection relation and the numbers of all the nodes, a regular expression of each node in the pentasaccharide core is calculated, and all the regular expressions are gathered to serve as an x-saccharide structure string code, wherein x is the number of nodes of each saccharide structure; based on the regular expressions, a string code of saccharide structures with the node number being x+1 is generated through an enumeration method and serves as an (x+1)-saccharidestructure string code; and according to the (x+1)-saccharide structure string code, redundancy of all the generated saccharide structures with the node number being x+1 are removed, the rationality ofthe structures is judged, the (x+1)-saccharide structures which are reasonable and non-redundant are output into a text file, and the text file is used as an N-saccharide structure base. Through theconstruction method and system, space overhead generated in a saccharide base enumeration process is saved, and the enumeration speed of the saccharide structures is effectively increased.