The effects of period phase perturbation of large aperture KDP crystal in middle spatial frequency are analyzed based on the results of experiments of Shenguang II. The period of phase perturbation of crystal reflection wavefront is near 20 mm, and the modulation amplitude is about 35 nm, the period of the third harmonics near field is about 12 mm, the contrast of strip is between 0.1 and 0.3, which leads to 3ω far field distortion and the probability of self-focusing increase. This cycle modulation at medium high frequency is possible caused by vacuum siphon in the process of crystal manufacture, and it needs to be verified in the follow-up experiment.