Both feature detection and point correspondence algorithms always heavily influence the performance of real-time tracking in general binocular systems. In this paper, we develop an infrared tracking system to reduce the deficiencies of feature detection. When this system is implemented in the operating room, light reflection from the metal instruments causes computational redundancy during point correspondence. General epipolar rectification with image registration techniques improves the efficiency of correspondence dramatically. The total amount of candidate correspondences can effectively be reduced by using the image registration method for point correspondence. Our algorithm takes the advantages of both rectification and image registration to achieve real-time tracking. Moreover, the proposed method improves accuracy by approximately 50% and efficiency by 100%, in comparison to general epipolar rectification.