Acute respiratory distress syndrome (ARDS) is severe respiratory failure in clinical practice, with a mortality rate as high as 40%. Injury of pulmonary endothelial cells and alveolar epithelial cells occurs during ARDS, and pulmonary endothelial injury results in endothelial barrier disruption, which usually occurs before epithelial injury. Especially, when harmful factors enter the blood, such as sepsis and hemorrhagic shock, the pulmonary endothelial cells are affected firstly. The injured endothelial cells may loss cell-to-cell connections and even die. After the endothelial barrier is disrupted, fluid and proteins cross the endothelial barrier, causing interstitial edema. The alveolar epithelium is more resistant to injury, and when the tight barrier of the epithelium is broken, fluids, proteins, neutrophils, and red blood cells in the interstitium enter the alveolar space. From this process, it is easy to find that the endothelium is the first barrier to prevent edema, therefore, the protection of endothelium is the key to the prevention and treatment of ARDS. In addition, the injured endothelial cells express selectin and cell adhesion molecules, promoting the recruitment of immune cells, which exacerbate the inflammatory response and pulmonary endothelial cell injury. Mesenchymal stem cells (MSCs) can be derived from umbilical cord, bone marrow, adipose and so on. Because of low immunogenicity, MSCs can be used for allogeneic transplantation and have great application potential in tissue repairing. Through paracrine effect, MSCs can promote cell survival and balance inflammatory response. MSCs infused intravenously can locate in lungs rapidly and interact with endothelial cells directly, thus MSCs have advantages in protecting pulmonary microvascular endothelial cells. Animal experiments and clinical trials have found that MSC transplantation can significantly improve the symptoms of ARDS and reduce inflammatory reactions and endothelial permeability. Mechanically, MSCs acts mainly through paracrine and immunomodulatory effects. Paracrine cytokines from MSCs can not only promote pulmonary endothelial proliferation, but also reduce inflammatory response and promote cell survival to maintain endothelial integrity. In addition to paracrine cytokines, extracellular vesicles of MSCs are rich in RNAs, proteins and bioactive substances, which can protect pulmonary endothelial cells by intercellular communication and substance transport. Furthermore, MSCs may protect pulmonary endothelial cells indirectly by regulating immune cells, such as reducing the formation of extracellular trapping network of neutrophils, regulating macrophage polarization and regulating Th17/Treg cell balance. Although the beneficial effects of MSCs are verified, much work still needs to be done. MSCs from different tissues have their own characteristics and the scope of application. Different lung diseases possess different endothelial injury mechanisms. Thus, determining the indications of MSCs derived from different tissues is the direction of pulmonary disease clinical trials. From the perspective of transplantation route, intravenous injection of MSCs may have better clinical application in pulmonary endothelial injury caused by endogenous harmful factors in blood. Previous reviews mostly focused on the protective effects of MSCs on alveolar epithelium. In this article, we focused on endothelial cells and reviewed the direct protective effects and mechanisms of MSCs on endothelium through paracrine cytokines and extracellular vesicles, and summarize the mechanisms by which MSCs may indirectly protect pulmonary endothelial cells by regulating immune cells.