An optical imaging based fully automatic stereo vision system for aircraft assembly online measurement is presented and analyzed. In this system, the relative position of the two cameras can easily calibrated by imaging an optical reference bar in different locations and orientations throughout the measurement space according to epipolar constraint and the certified distance of the features on the reference bar. For measurement, the system takes infrared LEDs which attached at measured object as imaging targets, and makes use of the measurement results of these feature points space coordinates to calculate the related positions of the assembly aircraft parts. Furthermore, using automatic infrared LED light intensity and CCD cameras exposure time improve the calibration and measurement accuracy. The effectiveness of the proposed system has been test by experiments.