The iron oxide nanoparticles are composed of nanostructured iron oxide molecules and organic (or inorganic) surface coatings, which have unique magnetic properties and excellent biocompatibility, and are widely used in medical field. As long as the diameter of iron oxide core is less than 10~15 nm, they exhibits superparamagnetism in a certain temperature range, which is often used for magnetic resonance imaging. Up to now, a variety of products based on superparamagnetic iron oxide nanoparticles have been approved for various clinical uses. So far, there is no effective method for tracing migration, distribution, and homing of the transplanted stem cells in human, heavily hampering the mechanism and efficacy researches of stem cell-based products. The combination of superparamagnetic iron oxide nanoparticles and magnetic resonance imaging technology brings a hope for clinical translation of stem cell tracing, which is expected to become “the gold standard” for stem cell tracing in future. However, there is no relevant nano-iron approved as clinical stem cell tracing markers in clinic setting so far. This article reviews research progresses of nano-iron particles in stem cell tracing clinical translation, the facing opportunities and challenges, also gives a prospects for the development in the future．