The measurement of pupil-positoin change in real-time precise automatic alignment of optical system is investigated. The translation data of the pupil is obtained by processing reference of phase-correlation algorithm and experimentally measured image; the measurement relative error is less than 0.4 pixel. In accordance with the various influencing factors such as the grey level change, noise, rotation and scaling, theoretical analysis and simulation test of the algorithm is performed. The results show that algorithm can overcome effect of inhomo-geneous distrbution of light intensity and severe noise, so that high measurement result can be obtained. After correction of the rotation and scaling corrected, the measurement precision remains in 1 pixel. The measurement method that superposed multi-image sum is taken as the reference image is proposed, the phase correlation SNR is enhanced by 88.6%, robutness is obviously increased.