The mechanical properties of each soil layer in multiple-structure thick overburden pervious foundation diverge significantly and specific questions that draw attention are quite different from each other. Based on the principle of Biot consolidation theory,the study takes soil non-liner rheological and the change of porosity, permeability coefficient, elastic modulus and poisson ratio at the consolidation deformation process of soil into account. The coupling process of seepage and stress fields of Daga hydropower station dam foundation is simulated by fluid-structure interaction module of ADINA to analyze mechanical properties and interaction of each layer. The research shows that the looser permeable soil on surface is the main seepage channel, also the inlet and outlet area of seepage and settlement deformation reflects area. Measures should be taken to improve the compression modulus in upstream and install the anti-filter layer and drainage facilities in downstream area. Fine sand layer in dam foundation is the main reason for dam foundation settlement, which plays a very leading role in the dam foundation settlement. Meanwhile, attention should be payed to the liquefaction properties of adverse impact on the dam foundation. Artesian aquifer in dam foundation produces up-holding force on the downstream side of the upper structure, and the destruction is small if the location is deep. Deep soil layer have a less effect on the seepage failure of dam foundation, but the effect can not be dismissed on settlement and seepage flow. Since in the permeability coefficient of sand gravel stratum and fine sand layer exists a modest distinction, the soil layer does not generate the contact erosion. In addition, the pore water pressure is dissipated at a rapidly-declining phase, and the dam foundation shows a stabletendency at rapid consolidation stage. Vertical cutoff wall can effectively decrease seepage gradient and seepage discharge, and the settlement deformation of dam foundation is controlled in upstream region of cuttoff wall. But the deformation of upstream dam foundation produces a large horizontal thrust to the cutoff wall, so the size of cutoff wall should be increased or the auxiliary seepage control measures shall be adoptedcorrespondly.