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Three-dimensional numerical manifold method for unconfined seepage analysis is proposed in this article. By constructing hydraulic potential functions of the manifold element, the element conductivity matrix and the global simultaneous equations for unconfined seepage analysis are derived in detail. The algorithm of locating the free surface and the formula for seepage forces are also given. Three-dimensional manifold method employs the tetrahedral mathematical meshes to cover the whole material volume. In the iterative process for locating the free surface, the manifold method can achieve an accurate seepage analysis of the saturated domain below the free surface with mathematical meshes unchanged. Since the shape of manifold elements can be arbitrary, the disadvantage of changing the permeability of transitional elements cut by the free surface in the conventional Finite Element Method (FEM) is removed, and the accuracy of locating the free surface can be ensured. Furthermore, the seepage force acting on the transitional elements can be accurately calculated by the simplex integration. Numerical results for a typical example demonstrate the validity of the proposed method.