This project presents the site-specific N-glycoproteomics dataset of aging mouse uterus tissues used to demonstrate and validate StrucGAP, a modular and scalable downstream analysis platform for glycoproteomics. Uterine samples were collected from 2- and 12-month-old C57BL/6 female mice (n = 15 per group), followed by protein extraction, tryptic digestion, TMT 10-plex labeling, intact glycopeptide enrichment, and LC-MS/MS analysis. A total of 20,251 unique intact glycopeptides (IGPs) were identified using the StrucGP search engine. The dataset captures detailed structural and quantitative glycosylation patterns across aging, enabling downstream analyses of glycan substructures, glycosylation site variation, and functional glycoproteomic annotation.