MRgHIFU treatment for liver requires a tracking technique to “lock on” to the focal spot at the target tissue region during respiratory-induced motion for targeting and temperature imaging. Here, we proposed a target tracking technique using template matching methods. A pre-operative, multi-slice sagittal image series under natural slow breathing was acquired, and a database, including a three-dimensional translation and deformation behavior of the liver and the target, was constructed. Intra-operative target tracking was performed by acquiring a single sagittal slice. The experimental results were demonstrated the feasibility of the three-dimensional target tracking technique using a template matching methods.