Double cut-off walls have been widely used in deep overburden foundation with alternating interloyered soils in Southwest China. However, how to determine the spacing and the layout of double cut-off walls, and the effect of seepage control need to be further investigated. In this paper, based on the unsaturated seepage theory, taking the deep overburden dam foundation with alternating interlayered soils as an example, double cut-off walls are experimentaly studied. The seepage discharge and exit gradient were obtained, and seepage control effect of cut-off walls under different layouts was discussed. Results show that the total seepage discharge and the exit gradient decrease with the distance. The seepage discharge of dam body is divided by the spacing of 13.2 and 16.5 cm, which increases at first and then decreases. Seepage discharge of dam foundation is divided by the spacing of 13.5 and 17.5 cm, which decreases at first and then increases. The wall with deeper penetration depth reduces the head of water more. The front and back walls reduce 37.5 percent and 50 percent, respectively, when the depth of two cut-off walls are same. It is found that given the same total penetration depth of two cut-off walls, the arrangement form with short in front and long in back decreases seepage discharge and controls exit gradient more effectively, which is therefore recommended for priority.