Endothelium plays a vital role in the logistics of the immune system, as well as the maintenance of the homeostasis. The major objective of this study is to unravel the relationship between expression changes of carbohydrate structures and the dysfunction of human umbilical vein endothelial cells (HUVEC) stimulated with tumor-conditioned medium (TCM), which is involved in tumor cell extravasation. Using flow cytometry (FCM) assay, the expression profiles of a selected group of 9 carbohydrate structures have been determined in HUVEC under control conditions and TCM-treated conditions, six of which increased significantly in expression after induction. Particularly, the expression level of beta-1,6-GlcNAc branching glycan was extremely higher after the stimulation. In parallel, the conformation change of HUVEC monolayer has been detected with inverted phase contrast microscopy and confocal microscopy. Under TCM stimulation, the actin cytoskeleton underwent rearrangement and formed abundant stress fiber within cells; therefore cell contraction was induced, which resulted in paracellular gap formation and barrier dysfunction. We furthered our study to investigate the mechanism underlying the conformation change of HUVEC. The results demonstrated that TCM induced the increase in beta-1,6-GlcNAc branching expression of PECAM-1, accompanied by the tyrosine phosphorylation of PECAM-1. The downstream effector RhoA was activated in consequence of the activation of PECAM-1. In conclusion, our results strongly suggested that the carbohydrate composition of endothelial cell surface is very important for the cells to exert their physiological effects correlated with cancer extravasation.