The estimation of the shifts between sub-images obtained in extended scene Shack-Hartmann wavefront sensing (SH-WFS) are the keys for calculating wavefront errors. The estimation can be got by parabolic interpolation algorithm and the accuracy can reach sub-pixel. The estimation can also be acquired by frequency-domain phase-shift algorithm and the accuracy can increase using frequency-domain iterative algorithm. Based on the later algorithm, the theoretical analysis, simulation and experiment are researched. The results show that the parabolic interpolation algorithm and frequency-domain iterative algorithm get close results in low signal-noise-ratio (SNR), but the later one performs better while SNR is higher than 41.