Magnetic resonance imaging (MRI) has been used as a powerful and indispensable tool in medical research and clinical diagnosis due to its high spatial resolution and non-limited penetration depth. The simultaneous use of positive and negative MRI imaging that employs the same contrast agents will significantly improve the detection accuracy. Here we report for the first time the development of multimodal iron oxide nanoparticles for targeted MRI of thrombosis using a combination of chemical and biological techniques.