The invention relates to an analytic method of a polysaccharide topological structure based on mass spectrometry. The method comprises the steps of obtaining a first grade mass spectrum containing experimental isotope outline information of precursor ions after conducting electrospray ionization and mass spectrometry on polysaccharide samples ready to be analyzed, and conducting cascade stage mass spectrum dissociation on the precursor ions of the first grade mass spectrum to obtain a second grade mass spectrum of corresponding fragment ions; conducting comparison between the experimental isotope outlines of the precursor ions and the theoretical database of the precursor ions to obtain multiple candidate polysaccharides which correspond to the precursor ions; and conducting comparison between the theoretical isotope outline of each theoretical fragment ion of each candidate polysaccharide and the experimental isotope outlines of the fragment ions observed in the second grade mass spectrum which corresponds to the candidate polysaccharides, and then the candidate polysaccharide which has the highest matching rate is the final polysaccharide ID. Compared with the prior art, the analytic method of polysaccharide topology is simple and clear, efficient and accurate, and is applicable to qualitative identification and quantitative analysis of the polysaccharide topological structure based on high resolution cascade stage mass spectrometry.