Superparamagnetic iron oxide nanoparticles (SPION) have emerged as a novel probe for noninvasive cell tracking using magnetic resonance imaging (MRI) and have a potential to a wide variety of medical researches and clinical investigations. In the present study, we report developed a method using coprecipitation of thermally cross-linking to synthesize heparin coated iron oxide nanoparticle (heparin-SPIO) as a biocompatible contrast agent for MRI and a new approach to efficiently label Ins-1 cells with the MRI probe. Sizes, crystal structures, and magnetic properties of the synthesized nanoparticles have been characterized. The newly synthesized heparin SPIOs with high stability, crystallinity, and saturated magnetization were efficiently internalized into Ins-1 and Raw 264.7 cells without cytotoxicity. Ins-1 cells that were transplanted in renal sub-capsular model of nude mouse were capable of being monitored using a clinical 3.0 T MR imager through detecting the heparin SPIOs, which were labeled onto the cells. These results indicate that heparin SPIOs have the great potential to the various applications as an MRI contrast agent for monitoring transplanted islet grafts in the clinical use in the future.