Wound repair and functional reconstruction are two key aspects for treatment of skin injury. Research on cell source for skin repair has become a focus of study. The immune rejection induced by allograft cells and the limited source of autologous epidermal stem cells have led to more attention on the multipotent adult progenitor cells (MAPC). In this study, we examined the influence of the local environment of skin injury on the migration and differentiation of MAPC in nude mice. The homing of MAPC to the wounds and the epidermal differentiation of MAPC were investigated by detecting the expression of specific antigens of rat major histocompatibility complex I (MHC-I) antigen and the tracing markers. Three weeks after transplantation, hair follicle-like structure appeared and rat MHC-I antigen was positive in the follicles of the healed skin. PKH26-labeled cells expressing cytokeratin were found in the regenerated follicle-like structures, sebaceous glands and sweat glands. Our findings indicate that MAPC can migrate to the skin injury site and the hair follicles, and participate in skin wound healing by differentiating into epidermal cells, which contributes to the theoretical research of MAPC plasticity and provides theoretical evidence for clinical application of transplantation therapy with MAPC.