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Periodontitis is a common chronic inflammatory disease, which causes the destruction of both the soft and mineralized tissues. However, current treatments such as bone graft materials, barrier membranes, and protein products all have difficulties in regenerating the complete periodontal tissue structure. Stem cell-based tissue engineering has now emerged as one of the most effective treatments for the patients suffering from periodontal diseases. Plants not only can be substrates for life processes, but also contain hormones or functional molecules. Numbers of preclinical studies have revealed that products from plant can be successfully applied in modulating proliferation and differentiation of human mesenchymal stem cells. Plant-derived substances can induce stem cells osteogenic differentiation, and they also possess angiogenic potency. Furthermore, in the field of tissue engineering, plant-derived compounds or plant extracts can be incorporated with biomaterials or utilized as biomaterials for cell transplantation. So it is speculated that botanical products may become a new perspective in stem cell-based periodontal regeneration. However, the lack of achieving predict clinical efficacy and quality control has been the major impediment to its extensive application. This review gives an overview of the prospect of applying different plant-derived substances in various human mesenchymal stem cells-based periodontal regeneration.