Currently, cell transplantation in combination with scaffold materials are one of the main strategies in periodontal bone tissue engineering. In periodontal bone tissues, the stiffness and spatial structure of tissues such as alveolar bone and cementum differ, and the difference in mechanical properties of scaffolds also has disparate effects on the proliferation and differentiation of stem cells. Accumulating evidence shows that mechanical stimulating factors such as matrix stiffness and scaffold topography modulate biological behaviors of various seeding cells, including adipose-derived stem cells and periodontal ligament stem cells. A hard matrix can promote cytoskeletal stretching of stem cells, leading to nuclear translocation of Yes-associated protein (YAP) and promoting osteogenic differentiation by upregulating alkaline phosphatase (ALP) and osteocalcin (OCN) via the Wnt/β-catenin pathway. The topologic structure of scaffolds can affect cell adhesion and cytoskeletal remodeling, increase the hardness of cells and promote the osteogenic differentiation of stem cells. In this paper, the effects of mechanical stimulation on the differentiation of stem cells in periodontal bone tissue engineering are reviewed.