Regenerative medicine aims to repair damaged tissues or organs, which is commonly employed in treating various refractory diseases. Current multimodal regenerative approaches include transplantation of healthy organs, tissues, or cells, stimulation of the body to activate the self-repair response in damaged tissues, and combined application of cells with biodegradable scaffolds to achieve functional tissues. Mesenchymal stem cells (MSCs), presenting in nearly all tissues, exhibiting characteristics such as easy accessibility, self-renewal capacity, multidirectional differentiation potential, and significant regenerative medicine applications. This article summarizes the applications of MSCs in regenerative medicine—primarily encompassing bone, skin, kidney, liver, heart, ovary, cornea, tracheal, and neural tissue repair—and addressing potential risks and considerations associated with their use, providing references for fundamental and clinical application research.