Pulmonary embolism (PE) is a pathological process of pulmonary artery or its branches blocked by free thrombus or other substances, which induce a significant morbidity and mortality. Endothelial cell injury is one of the most important mechanisms of pulmonary embolism which indicate that it may be helpful of endothelial cell repair in PE therapy. ,However, it needs to prove by evidence-based medicine. In this review, we talk about the drug of endothelial cells protection or repair and anti-thrombus in PE treatment based on the mechanism of endothelial cell injury.