Harmonic phase (HARP) analysis has been used in tagged magnetic resonance imaging (MRI) to measure two-dimensional (2D) in-plane motion and strain, and was recently applied in characterizing the motion of tongue during speech. The 3D-HARP method extended the HARP method to track three-dimensional (3D) cardiac motion from short- and longaxis tagged MR images by diffusing 2D in-plane motion on a sparse 3D mesh. In this paper, we propose a new 3D-HARP method to calculate the 3D tongue motion from three orthogonal tag orientations imaged within sagittal, coronal, and axial image planes. Our method iteratively tracks 2D in-plane motions on points on a compact mesh using 2D-HARP followed by thin-plate spline (TPS) interpolation to extend the 2D motion to the whole mesh. Experiments on real tongue data show that our method is capable of accurate motion tracking in simple utterances.