The traditional vertical seepage control system, which is composed of core-wall and the cutoff wall, follows the design concept that the cutoff wall is deepened with the deepening of the deep overburden layer. So, it will prolong the construction period of the cutoff wall and makes the construction quality difficult to be guaranteed when building the dam in the deep overburden layer. Therefore, a new space orthogonal seepage control system is proposed, which is applied to the high rock-fill dam on the deep overburden layer. And taking a project as an example, a series of exploratory calculations were carried out using the SEEP/W. The analysis shows that, if the construction quality of the horizontal impervious layer can be guaranteed, the space orthogonal seepage control system can meet the requirement of the total seepage flow and the infiltration ratio, even better than the traditional seepage control system. The proposed orthogonal seepage control system can remarkably reduce the thickness or the depth of the main cutoff wall, and reduce the amount of engineering, shorten the construction period.