Magnetic resonance imaging (MRI) holds promise for the early clinical diagnosis of various diseases, but most clinical MR techniques require the use of a contrast medium. Several nanomaterial (NM) mediated contrast agents (CAs) are widely used as T1- and T2-based MR contrast agents for clinical and non-clinical applications. Unfortunately, most NM-based CAs are toxic or non-biocompatible, restricting their practical/clinical applications. Therefore, the development of nontoxic and biocompatible CAs for clinical MRI diagnosis is highly desired. To this end, several biocompatible and biomimetic strategies have been developed to offer long blood circulation time, significant biocompatibility, in vivo biodistribution and high contrast ability for efficient imaging. However, detailed review reports on biocompatible NMs, specifically for MR imaging have not yet been summarized. Thus, in the present review we summarize various surface coating strategies (such as polymers, proteins, cell membranes, etc.) to achieve biocompatible NPs, providing a detailed discussion of advances and future prospects for safe MRI imaging.