In this paper, the visco-elastic boundary processing method for dynamic analysis of earth-rock fill dam on deep overburden layer and the traditional fixed boundary processing method were used to do the dynamic response analysis of one earth-rock fill dam on super-deep overburden layer under earthquake. The influencing law of boundary processing way and foundation cut-off scale on dynamic analysis results was studied firstly, and the boundary processing method of dam and foundation system which is the study subject in this paper was investigated carefully then. The results show that, the distribution law of acceleration response in dam and foundation system is consistent basically in different boundary processing ways. Dynamic response level of dam in visco-elastic boundary condition is lower than it in fixed boundary condition, and the calculation results in fixed boundary condition is somewhat safe. The acceleration response level of dam declines in different boundary processing ways as the increasing of overburden layer foundation scale, and the calculation results in fixed boundary processing way and visco-elastic boundary processing way tend to closed when the foundation scale is large enough. For the earth-rock fill dam and foundation system in this paper, the reasonable boundary processing method of system dynamic analysis is that the interface of deep overburden soil layer and base-rock is selected to be the bottom boundary, two lateral cut-off boundaries are 3-5 times of dam and foundation height from two dam feet, and the boundary processing way is the fixed boundary condition.