In this paper, to decrease the impact of the speckle noise on medical image registration, a new nano-material as a dual-modality contrast agent, magnetic microbubbles (MMBs) were introduced in both ultrasound (US) and magnetic resonance imaging (MRI) procedure to enhance the most important information of interest. Then, a classical optical flow model between US image and MR was adopted, and the vector flow field was solved by using the Coarse-to-fine Gaussian pyramid. The multi-group comparison experiments showed that US-MRI registration using MMBs combined with the method mentioned was a feasible way for gaining better medical image registration.