The structures of two-layer silicene and the 4H-modified silicon carbide (SiC) film supporting it, which act as the anode of a lithium-ion battery, are studied by the molecular dynamics method. The behavior of such a combined anode is considered under conditions of its vertical filling with lithium. The silicene sheets contain vacancy defects in the form of bi-, tri-, and hexavacancies. Lithium ions directed perpendicularly to the silicene plane deposited on the silicene sheets remain in the silicene channel and partially penetrate the substrate surface. The vertical displacements of atoms in the top sheet of silicene after lithium intercalation significantly exceed the corresponding displacements in the bottom sheet in contact with the substrate. The construction of Voronoi polyhedra (VP) separately for the Si- and C-subsystems of SiC make it possible to reveal the structural features of each of the subsystems of the studied two-dimensional layered structure.