Abstract: Organ transplantation is a crucial therapeutic approach for saving patients with end-stage organ failure. However, transplant organs are frequently subjected to various pathological insults, such as ischemia-reperfusion injury and rejection during the processes of procurement, preservation and revascularization, which severely compromise graft survival and function. Endothelial dysfunction represents a core determinant of graft function and transplant outcomes. Factors including ischemia-reperfusion injury, rejection, immunosuppressive drug use and cytomegalovirus infection drive endothelial dysregulation through diverse acute or chronic mechanisms. In the acute phase, endothelial injury contributes to delayed graft function and acute rejection, while in the chronic phase, it manifests as graft vasculopathy, ultimately leading to graft failure. This review summarizes the key pathophysiological mechanisms underlying endothelial injury in organ transplantation, its clinical consequences, and preventive and therapeutic strategies, aiming to provide insights for improving endothelial function and transplant outcomes.