According to the experimental results from atmospheric surface-layer and turbulence cell, a cubic model of ellipsoid depicting large-scale structure is put forward. The effect of large-scale structure on wave-front during light transporting is computed and analyzed, and compared with the small-scale effect. On the same parameters of model, the effect on phase structure function of wave front is a little larger when ray is parallel to the discontinuous plane than ray is perpendicular to the discontinuous plane. Generally, the effect is small, but when the large-scale structure is one-dimensional and ray goes parallel to the discontinuous plane, the effect is large.