Whey proteins are N-glycosylated proteins that play important roles in a variety of biological processes including immune defense. However, the N-glycosylation of yak colostrum (YC) and mature milk (YM) whey proteins is unknown. Therefore, this study systematically compared and analyzed YC and YM whey N-glycoproteomes using the 4D label-free technique. We identified 162 glycoproteins, 222 glycosylated peptides, and 234 glycosylation sites in YC and YM, of which 59 glycoproteins were differentially expressed in YC and YM. According to gene ontology annotation and KEGG pathway metabolism analysis, the differentially expressed N-glycoproteins were highly enriched in "cell adhesion", "extracellular region", and "calcium binding", and were mainly involved in the extracellular matrix (ECM)-receptor interaction pathway. The immunity-related N-glycoproteins, such as platelet glycoprotein 4 (CD36) and polymeric immunoglobulin receptor (PIGR), were observed to be different between YC and YM. The results revealed the glycosylation sites, composition, and biological functions of YC and YM whey N-glycoprotein, which supplemented our understanding of the N-glycosylation of yak whey proteins.