Abstract: The earth-rock dams built on deep overburden layers often use a closed seepage control system which is composed of core wall of dam body and impervious wall of dam foundation. Uneven settlement will occur between concrete core wall base, impervious wall and the adjacent soil, which leads to the fracture of concrete base and the shear failure of dam body and its foundation when the asphalt concrete core wall is used in dam body and a closed impervious wall is used in dam foundation. Taking an earth-rock dam on a deep overburden layer as a study object, a three-dimensional finite element model is establised, and the deformations and stresses of the dam body and its foundation are analyzed by use of the nonlinear finite element method. By comparing the analyses of deformation compatibility of dam body and its foundation and the stresses of core wall with its base and impervious wall, a reasonable connection type is recommended for the core wall dams, which should reserve a gap between the base and the impervious wall for an earth-rock dam built on deep overburden layer which uses a closed seepage control system. The size of the reserved gap is related to the thickness of the overburden layer and its mechanical properties as well as the elastic modulus of the impervious wall, and it requires computational analysis for determination.