In recent years, with the rapid development of stem cells science, mesenchymal stem cells(MSCs)have become a research hotspot. Bone marrow mesenchymal stem cells(BMSCs)are MSCs that derived from bone marrow with some advantages, such as the potential of multi-directional differentiation, low immunogenicity, promoting damage repair and stable performance. The study by many scholars found that BMSCs are promising special cells in the field of medicine, and BMSCs have been widely used in almost every system in treatment of disease. For treatment of corneal disease, ophthalmology scholars found that BMSCs have already become a kind of seed cells with clinical and science value. BMSCs brought promising to the patients who have complex corneal disease. In this paper, we introduce the function of BMSCs on the treatment of corneal injury and corneal allograft rejection.