The application of Gd-based contrast agent is widely broad for magnetic resonance imaging in clinic diagnosis. However, the toxicity of Gd-based contrast agent still cannot be ignored. Therefore, most researchers have made a great effort to find low toxic contrast agent. Iron oxide nanoparticles(IONP) have a great dark contrast effects in magnetic resonance imaging(MRI) due to their superparamagnetic properties, and they also have good biocompatibility. With the rapid development of biomaterials and molecular image technology, the application of IONP in MRI has become more and more broad. In recent years, IONP has made great progress in dual-modal imaging. What’s more, IONP is not only used to clinical diagnosis, but also in treatment. It offers some new strategies for the treatment of disease. Based on the magnetic resonance imaging mechanism and preparation, surface modification of IONP, this review elaborates the research progress of IONP in magnetic resonance imaging in recent years.