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Hair follicle mesenchymal stem cells (HFMSCs) are slow cycling label retaining cells with self-regeneration ability, high proliferative potential, and multi-directional differentiation. HFMSCs can induce and promote the regeneration of the epidermis, hair follicles and sebaceous glands. HFMSCs have important advantages in regenerative medicine because of their abundance, wide availability, expansion in vitro, no genetic manipulation, no tumor formation and no ethical restriction. The synergy and antagonism between Wnt and other signaling pathways such as Shh, Notch and BMP signaling pathways play a crucial role in the regulation of stem cell homeostasis, epidermal development and hair follicle regeneration. The dysregulation of these pathways may result in hair loss diseases or skin tumors. This paper summarizes the classification and some specific biomarkers of HFMSCs, and discusses the induction of HFMSCs and the biomolecular pathways that affect hair regeneration, so as to shed light on the treatment strategies of hair diseases.