To study the influence of the spatial irregular distribution of the fundamental beams on the measurement of pulse duration of the second-order autocorrelator, the principle of single-shot second-order autocorrelator was analyzed. The influences of periodical modulation and local dim /bright region on the measurement of pulse duration were discussed numerically. The results show that when the intensity was modulated periodically, at certain extent the higher the modulation and the sparser the strips, the bigger the autocorrelator measurement warp will be. When the intensity was modulated by local dim /bright region and the dim region is not large, the wider the dim region or the narrower the bright region, as well as the higher the modulation, the bigger the autocorrelator measurement warp will be.