The mechanical properties of every soil layer in multiple-structure thick overburden pervious foundation diverge significantly and specific problems that draw attention are diverse in range, which requires further study. This paper derived from the principle of Biot consolidation theory takes into account soil non-liner rheological and the change of porosity, permeability coefficient, elastic modulus and poisson ratio at the consolidation deformation process of soil. 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, inlet and outlet area of seepage and settlement deformation reflects area, and 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 of dam foundation settlement, which plays a leading role in dam foundation settlement, at the same time, attention should be called to the liquefaction properties of adverse impact on the dam foundation. Artesian aquifer in dam foundation produce 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 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 most of pore water pressure is dissipated at rapidly-declining phase, dam foundation shows a tendency of stability 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 produce a large horizontal thrust to cutoff wall, so the size of cutoff wall should be increased or auxiliary seepage control measures adopted to contain that.