Effective methods for extending the storage capacity of tailings for a mining company include expanding and increasing the height of the tailings dam. However, this change could lead to an uplift in the phreatic line and a decrease in the slope stability. In this paper, a new drainage system combining a horizontal drainage pipe with an upward bending slotted pipe was proposed and applied to the design of a seepage-proof system for the Xigou tailings dam with an increased height. To accurately simulate the performance of the seepage control system, a three-dimensional finite element model was established on the basis of a geological investigation of the site conditions. In this work, a substructure technique was used to model the drainage pipe with a small radius and dense spacing to reduce the difficulty in mesh generation, and a back-analysis method called MPSO-BP (modified particle swarm optimization algorithm and a back propagation neural network) was used to correct the measured permeability coefficients. The results show that the new drainage system can effectively dissipate the seepage pressure, decrease the phreatic surface, and improve the safety factors of the slope stability. The proposed drainage system can also meet the seepage stability requirements of the higher tailings dam. Additionally, this system can be widely deployed in similar projects.