In this paper, proposed is an embedded automatic locating and tracking system based on eye corneal endothelial cell analyzer manually locating and tracking eyeball. It is adopted the combining method of image processing and infrared distance measurement, then the real-time locating and tracking experiment was performed on the target object and the automatic locating and tracking function was realized on target objects. The locating errors of X and Y axis are not more than seven pixels and the positioning error of Z axis is not more than 3mm. The method is verified to own high reliability, real-time and practicability according to clinical tests.