In the highprecision electrooptical tracking and pointing system, fast steering mirror is the core component in the fine channel. It can realize the resolution of the rotation angle of sub micro radian. The measurement error has a direct influence on the control precision of the pointing and tracking system, in which the height of the FSM reflector lens affects the error significantly, and it must be compensated and corrected in the precision tracking control. Based on the measurement model of one type of turntable equipped with a fast steering mirror of which measuring accuracy is about ±20 μrad , the error model induced by the reflector lens’ height is deduced and using the least squares estimation algorithm of system identification to extract the error characteristic parameters. The experimental results show that the influence of lens’ height on the error is reduced to ±2 μrad.