Real time magnetic resonance (MR) thermometry provides continuous temperature mapping inside the human body and allows precise monitor and control of thermal therapies. An accurate motion estimation is required on mobile targets. However, the assessment of the estimated motion accuracy is difficult since the real target motion is unknown. In this paper, existing criteria based only on anatomical image similarity are demonstrated to be insufficient. A new criterion is introduced, which is based on the phase image similarity. The proposed criterion was evaluated on a moving phantom and compared to the real motion and established criteria based on anatomical image. It exhibits better consistency of motion estimation assessment.