Stem cell therapy holds great promise in tissue regeneration and reconstruction. However, the underlying mechanisms remain elusive due to the lack of effective and noninvasive approaches during therapeutic processes. Within different strategies of molecular imaging, lanthanide-based up-conversion nanoparticles (UCNP) have been explored as imaging agents for luminescence imaging, magnetic resonance imaging (MRI) and computerized tomography (CT). As luminophore, UCNPs are preferable to other bioimaging probes. In this paper, the development history, preparation, the research status of stem cell tracer and the implications of tumor related research of UCNP were reviewed.