Stem cell therapy has shown great clinical potential in oncology, injury, inflammation, and cardiovascular disease. However, due to the technical limitations of the in vivo visualization of transplanted stem cells, the therapeutic mechanisms and biosafety of stem cells in vivo are poorly defined, which limits the speed of clinical translation. The commonly used methods for the in vivo tracing of stem cells currently include optical imaging, magnetic resonance imaging (MRI), and nuclear medicine imaging. However, nuclear medicine imaging involves radioactive materials, MRI has low resolution at the cellular level, and optical imaging has poor tissue penetration in vivo. It is difficult for a single imaging method to simultaneously achieve the high penetration, high resolution, and noninvasiveness needed for in vivo imaging. However, multimodal imaging combines the advantages of different imaging modalities to determine the fate of stem cells in vivo in a multidimensional way. This review provides an overview of various multimodal imaging technologies and labeling methods commonly used for tracing stem cells, including optical imaging, MRI, and the combination of the two, while explaining the principles involved, comparing the advantages and disadvantages of different combination schemes, and discussing the challenges and prospects of human stem cell tracking techniques.