Mesenchymal stem cells (MSCs) are a type of pluripotent stem cells originating from the mesoderm, known for their capability to differentiate into various specific tissue cell types and fulfill corresponding physiological roles. Furthermore, MSCs are essential in modulating the tissue microenvironment through the release of soluble factors that can modify the local inflammatory conditions of injured tissues. As a result, MSCs show considerable promise for therapeutic use in a range of traumatic scenarios, including but not limited to liver damage, myocardial infarction, neurological conditions, lung trauma, kidney injuries, and disorders affecting the female reproductive system. They play a key role in alleviating cell apoptosis, sustaining cell survival, encouraging proliferation, enhancing the inflammatory milieu, minimizing tissue fibrosis, and supporting vascular regeneration. These mechanisms are crucial for controlling excessive and persistent inflammatory reactions that arise after organ injury, which may lead to cell death and hindered blood circulation, ultimately causing fibrosis and weakened organ functionality. Additionally, MSCs are gradually being incorporated into clinical settings, where careful considerations regarding methods of administration, dosing, safety, and effectiveness are vital for achieving optimal clinical results. This review provides an overview of the mechanisms by which mesenchymal stem cells aid in the repair of major bodily organs. We also examine their current status, obstacles, and pertinent issues concerning clinical applications.