In view of the problems that existing research lacks an analysis on the optimal depth of cutoff walls in ultra-deep multilayer foundations containing an impermeable layer, and the influence laws of seepage under high external water pressure remain unclear, a generalized vertical anti-seepage model was established based on a hydropower project. By analyzing the seepage fields of the dam foundation under different cutoff wall depths, the influence laws of cutoff wall depth variations on the seepage field of the dam foundation in ultra-deep complex multilayer foundations were discussed, and on this basis, an optimal cutoff wall depth satisfying the standards of both soil seepage stability and seepage discharge control was proposed. The results indicate that the presence or absence of an impermeable layer in ultra-deep complex multilayer foundations significantly influences the evolution laws of the maximum hydraulic gradient at the cutoff wall tip. When the dam foundation does not contain an impermeable layer, the maximum hydraulic gradient at the cutoff wall tip shows a U-shaped trend with an increase in the penetration ratio and changes significantly when the penetration ratio is less than 0.2 or greater than 0.7. When the dam foundation contains an impermeable layer, above the impermeable layer, the maximum hydraulic gradient at the cutoff wall tip shows a U-shaped trend with an increase in the penetration ratio and changes significantly when the penetration ratio is less than 0.2 or greater than 0.7; within the impermeable layer, the maximum hydraulic gradient at the cutoff wall tip decreases rapidly with an increase in the penetration ratio; below the impermeable layer, the maximum hydraulic gradient at the cutoff wall tip increases slowly with an increase in the penetration ratio and increases rapidly when the penetration ratio is greater than 0.7. Considering the possible inhomogeneity and uncertainty in the deep parts of the ultra-deep overburden foundation, combined with existing engineering cases, a final cutoff wall depth of 200 m is recommended.