Dental-derived stem cells, an important research target in tissue engineering, have excellent proliferation ability and multi-directional differentiation potential. In recent years, an increasing number of odontogenic stem cells have been discovered, including dental pulp stem cells (DPSCs), stem cells from exfoliated deciduous tooth (SHEDs), apical papilla stem cells (SCAPs), dental follicle precursor cells (DFPCs) and periodontal ligament stem cells (PDLSCs). Due to the advantages of abundant sources, safe and effective, these stem cells have significant application prospects in tissue regeneration. The biological functions of odontogenic stem cells are regulated in many ways. Epigenetic regulation means changing the expression level and function of a gene without changing its sequence. Epigenetic regulation is involved in many biological processes, such as embryonic development, bone homeostasis, and stem cell fate. Existing studies have shown that odontogenic stem cells are also regulated by epigenetic modifications. Referring to replacing damaged pulp and periodontal tissue and restoring the tissue structure and function under normal physiological conditions, pulp regeneration and periodontal regeneration has better therapeutic effect than traditional treatments. This article reviews the recent research progress on the epigenetic regulation mechanism of odontogenic stem cells, and describes the potential applications of odontogenic stem cells-based epigenetic regulation in dental pulp and periodontal regeneration.