Stem cell therapy provides great promising therapeutic benefits for various neurological disorders. Cell transplantation has emerged as cell replacement application for nerve damage. Recently, nanomaterials obtain wide development in various industrial and medical fields, and nanoparticles have been applied to neuro-medical field for tracking and treating nervous system diseases. Combining stem cell with nanotechnology has raised more and more attentions; and it has demonstrated that it has huge effects on clinical diagnosis and therapeutics in multiple central nervous system diseases, meanwhile, improving prognosis. This review gives a brief overview of the application of nanomaterials in stem cell therapy for neurological diseases. Nanoparticles not only promote stem cell proliferation and differentiation in vitro or in vivo, but also play dominant roles in stem cell imaging and tracking. Furthermore, via delivering genes or drugs, nanoparticles can participate in stem cell therapeutic applications for various neurological diseases, such as ischemic stroke, spinal cord injury (SCI), multiple sclerosis (MS), Parkinson's disease (PD), Alzheimer's disease (AD) and gliomas. However, nanoparticles have potential cytotoxic effects on nerve cells, which are related to their physicochemical properties. Above all, nano-stem cell-based therapy as a promising strategy has the ability to affect neuronal repair and regeneration in the central nervous system.