Abstract: The sand liquefaction potential is evaluated with the in-situ test data of one single borehole in the relative codes, however, the real three-dimensional structure of the engineering site is very complex. It is helpful to increase the accuracy of the sand liquefaction evaluation by studying the effect of the soil layer structure on the liquefaction. By analyzing the distribution of the sites of the sand liquefaction manifestation caused in Songyuan M_S5.7 earthquake on the 28 May, 2008 and the 2010−2011 Canterbury earthquake sequence, it is discovered that most of the sites are located on the inside bend of the meandering river. The dualstructure exists in the point bar formed by the lateral erosion of the outside bend and the deposition of the inside bend. The impermeable（including weakly permeable） clay layer is covered on top of the saturated fine sand, which is easy to cause the accumulation of the excess pore pressure. The discontinuous distribution of the impermeable clay layer is obvious in the braided fluvial facies. The simplified model is built for soil layer structures with the different fluvial sedimentary facies. The FLAC3D software is used to study the mechanism of the accumulation and dissipation of the pore pressure, and the seepage flow process. The distribution of sand liquefaction manifestation and the ground surface deformation is highly affected by the the soil layer structure with the fluvial sedimentary facies. It is necessary to consider the influence of the soil layer structure in the sand liquefaction evaluation methods on the basis of engineering geological zoning.