Stem cells are a group of undifferentiated cells with indefinite self-renewal and pluripotent differentiation ability. They are able to differentiate into precursor/progenitor cells and a variety of cell types and further regenerate new cells to be involved in the repair and rebuilding of injured tissue. Therefore, stem cells are becoming the major research objects in the study on tissue engineering therapy and regenerative medicine. As a sense organ composed of several kinds of neurons and other cells, eyes possesse the dominant superiority in stem cell transplantation therapy because of its good operation controllability and visuality, less demand for seed cells and low rejection after transplantation. These advantages have aroused growing interesting of the fundamental research and clinical trail in stem cell transplantation for irreversible eye diseases. Some exciting advances in the field of stem cell fundamental research, several phase I/II clinical trials are in progress. The patients with degenerative eye diseases for phase I clinical trials are in recruiting in China to evaluate future curative effect and security of stem cell-based therapies. Currently, several issues in stem cell-based eye disease therapies are still pending. We discuss the updated development of stem cell-based transplantation in ophthalmology and future researching direction in order to help ophthalmological researchers to understand the concepts and research strategies.