N-glycosylation, a critical post-translational modification (PTM), plays an essential role in proper protein folding within the Endoplasmic Reticulum (ER) and for stabilization of mature glycoproteins. Despite its importance for fundamental biology and in the biopharmaceutical industry, our understanding of the site-specific role of N-glycosylation on protein stability is still lacking. Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS) facilitates global analysis of proteoforms and site-specific measurement of PTMs, providing the possibility to identify and quantify site-specific N-glycosylation on proteins with high throughput and sensitivity. Our study developed a strategy to discover the impact of specific N-glycosylation sites on protein stability by thermal glycoproteome profiling. By perturbing the N-glycosylation process, we generated glycoproteoforms with and without N-glycosylation at specific sites. Profiling these partially N-glycosylated glycoproteoforms over a temperature gradient enabled us to discover functional N-glycosylation sites based on changes in site-specific N-glycosylation occupancy of the soluble fraction post-thermal treatment. The established method provides an efficient strategy to map functional PTMs that affect protein stability, with potential applications in exploring the impact of site-specific glycosylation on protein-protein or protein-ligand interactions, in enhancing the stability of biologics, and in biomarker discovery.