The invention relates to the field of polymer material and analysis, and relates to organic-inorganic hybrid core-shell-structured microsphere particles, and a preparation and an application thereof. According to the invention, inorganic silica gel particles are adopted as cores, and are modified with a silanization agent; with a thiol-ene click chemistry technology, 3-allyloxy-2-hydroxy-1-propanesulfonic acid and methylene diacrylamide are wrapped on the surfaces of the cores, such that the organic-inorganic hybrid core-shell-structured nano / micro particles with smooth surface and with hydrophilic functional groups such as hydroxyl group, sulfonic acid group, amide and the like are formed. According to the invention, the hydrophilic functional groups such as hydroxyl group, sulfonic acid group, amide and the like are introduced to the surface of the material through the thiol-ene method, such that the defects of complicated steps and low reaction efficiency of a traditional post-modification method are solved, and a polymer three-dimensional-structured hydrophilic layer is formed. Better advantage is shown when the particles are used in hydrophilic chromatography. The microsphere particles can be used in hydrophilic interaction chromatography for separating and enriching glycopeptide, and have good practical value and application prospect in the fields of separation analysis and sugar proteomics.