A novel hierarchically ordered macro/mesoporous silica was functionalized with polyboronic acid (HOMMS@PolyVPBA). This composite possesses the attractive features of high surface area and large accessible porosity, and was applied to enrich glycopeptides. Here the HOMMS material was introduced into glycoproteome for the first time. The HOMMS@PolyVPBA gave remarkable selectivity for glycopeptides even at a low molar ratio of glycopeptides/nonglycopeptides (1:50) with a very rapid enrichment speed (only 10 min) and low detection (1 ng μL−1). Therefore the synthetic HOMMS@PolyVPBA might be a promising selective enrichment material for glycoproteome analysis.