Deep overburden distributes widely in rivers of our country, in which case the study is of great significance to speed up our country water conservancy and hydropower project. To build a dam on the deep overburden foundation, the first problem to solve is the seepage of the dam foundation. In this paper, two-dimensional numerical seepage analysis methods is used for project instances. The analysed result shows that it can decrease the amount of seepage when the length of clay waterproof blanket on the deep overburden foundation is 4 times upstream water head, that it doesn’t effect the amount of seepage when its length is more than 4 times upstream water head；that it can receive better effect of anti-seepage when the depth of cut-off wall is over 3/4 times thickness of deep overburden, and that it can cut off water flow reliably and effectively when the deep overburden are completely closed by the cut-off wall.