Currently, stem cell nanotechnology is one of the novel and exciting fields. Certain experimental studies conducted on the interaction of stem cells with nanostructures or nanomaterials have made significant progress. The significance of nanostructures, nanotechnology, and nanomaterials in the development of stem cell-based therapies for degenerative diseases and injuries has been well established. Specifically, the structure and properties of nanomaterials affecting the propagation and differentiation of stem cells have become a new interdisciplinary frontier in material science and regeneration medicines. In the current review, we highlight the recent major progress in this field, explore the application prospects, and discuss the issues, approaches, and challenges, to improve the applications of nanotechnology in the research and development of stem cells.