The deep anti-sliding stability of concrete gravity dam under seismic action is an issue receiving much concerns in hydro-structure design. In this paper, an analysis method for the deep anti-sliding dynamic stability based on rigid body limit equilibrium method and finite element method is proposed and corresponding numerical process is formulated. Firstly, the radiation damping effect is considered by setting a viscous-spring artificial boundary condition in the foundation model; the seismic wave velocity and the arrival time of incident wave are set different by partitions to reflect the non-uniformity of rock strata. Furthermore, the factor of safety is calculated by decomposing external load into sliding force and drag force in the rigid finite element result by directly calculating the internal force of cross-section in the model with double sliding surfaces recommended in specification. Subsequently, the two key parameters of the model with double sliding surfaces are determined through sensitivity analysis, and the effects of foundation’s uniformity on deformation and stability of the structure are compared. The proposed method is verified to be effective by a calculation case study of Xiaonanhai gravity dam.