Stem cell-based therapies have been shown potential in regenerative medicine. In these cells, mesenchymal stem cells (MSCs) have the ability of self-renewal and being differentiated into different types of cells, such as cardiovascular cells. Moreover, MSCs have low immunogenicity and immunomodulatory properties, and can protect the myocardium, which are ideal qualities for cardiovascular repair. Transplanting mesenchymal stem cells has demonstrated improved outcomes for treating cardiovascular diseases in preclinical trials. However, there still are some challenges, such as their low rate of migration to the ischemic myocardium, low tissue retention, and low survival rate after the transplantation. To solve these problems, an ideal method should be developed to precisely and quantitatively monitor the viability of the transplanted cells in vivo for providing the guidance of clinical translation. Cell imaging is an ideal method, but requires a suitable contrast agent to label and track the cells. This article reviews the uses of nanoparticles as contrast agents for tracking MSCs and the challenges of clinical use of MSCs in the potential treatment of cardiovascular diseases.