Xenotransplantation using porcine organs is a potential solution to bridge the gap between donors and recipients, but difference in glycosylation between humans and porcine limit successful clinical trials. Recent studies have shown that representative non-human glycan moieties such as galactose-α1,3-galactose(α-gal), NeuGc, and SDa antigens act as epitopes triggering antibody-mediated rejection (AMR). NeuGc leads to several inflammatory disorders and α-gal is known to cause more severe hypersensitivity reactions. Furthermore, it is essential to identify the glycan antigens adorned on the surface because endothelial cells interact first with the recipient's immune component during the xenotransplantation process. Despite the emphasis on the importance of glycans in the immune system, studies on comprehensive characterization of glycosylation including the structure of xeno-glycan antigens in porcine, a representative xenotransplantation model, are insufficient. Here, we performed overall glycan profiling and structural analysis of glycans with non-human moieties in porcine aorta endothelial cells. We could identify various glycan isomers and heterogeneity characteristics by accurate masses, retention times, LC/MS/MS, and exoglycosidase digestion. The major components were di-NeuAc-sialylated glycans in endothelial cells. In particular, non-human glycans, which can cause problems during trans plantation, were present in a small amount less than 10%. NeuGc-sialylated glycan ratios in cell are around 4%, A glycosylated unique form in which sialic acid attached to antennal N-acetyl glucosamine (HexNAc) is identified in aorta endothelial cells. The α-gal containing glycans were confirmed by not only MS/MS spectra but also α-gal glycan removal using galactosidase that breaks gal α1-3 linkages at the terminal in LC/MS chromatogram. Our data could be the reference for monitoring changes in glycan antigens in glycoengineering models for xenotransplantation and providing information for mammalian glycome studies.