Multipotent mesenchymal stem cells have shown great promise for application in regenerative medicine owing to their particular therapeutic effects, such as significant self-renewability, low immunogenicity, and ability to differentiate into a variety of specialized cells. However, there remain certain complicated and unavoidable problems that limit their further development and application. One of the challenges is to noninvasively monitor the delivery and biodistribution of transplanted stem cells during treatment without relying on behavioral endpoints or tissue histology, and it is important to explore the potential mechanisms to clarify how stem cells work in vivo. To solve these problems, various nanoparticles (NPs) and their corresponding imaging methods have been developed recently and have made great progress. In this review, we mainly discuss NPs used to label stem cells and their toxic effects on the latter, the imaging techniques to detect such NPs, and the current existing challenges in this field.