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In decades, stem cell nanotechnology has become a new promising field for stem cell research and development. So, stem cell nanotechnology has attracted lots of researchers’ attention and made great progress. The unique properties of nanomaterials and nanostructures which applied in the fundamental research of stem cell-based therapies have been recognized. Nanomaterials and nanotechnology have been highlighted as promising candidates for efficient control over proliferation and differentiation of stem cells, revolutionizing the treatment of neurodegenerative disorders, neuroprotection in traumatic brain injury, improving the osteospecific differentiation and function, tissue engineering scaffold, dental implant application, drug delivery, gene therapy and cell imaging or tracking. Here we summarize the main progress in this field, explore the application prospects in injuries, diseases, regenerative medicine, etc. and discuss the methods and challenges with the aim of improving application of nanotechnology in the stem cell research and development.