The present invention discloses a vertical interconnection structure for three-dimensional package based on aluminum substrates and a preparation method thereof. The structure comprises at least two layers of functionalized aluminum substrates. Each of the aluminum substrates comprises an aluminum through column, an aluminum semi-through column, a grounded aluminum column, a chip embedded cavity, an aluminum buried grounded layer and an aluminum embedded interconnection line. The vertical interconnection structure comprises embedded chips which are embedded in the chip embedded cavities of the functionalized aluminum substrates, film interconnection lines whose two ends are connected to the embedded chips and the aluminum through columns, intermetallic compound vertical interconnect lines whose two ends are connected to the aluminum through columns of two adjacent layers of functionalized aluminum substrates, and dielectric layers which are arranged at the surfaces of the functionalized aluminum substrates. The method comprises the preparation of the functionalized aluminum plate, the surface mounting of the embedded chips, the preparation of the film interconnection lines, the preparation of the dielectric layers, the deposition of the intermetallic compound, and the 3D stacked vertical interconnection. According to the vertical interconnection structure and the preparation method, the package efficiency and interconnection density are raised, and the intermetallic compound vertical interconnection is used to achieve the effect of 'low temperature preparation and high temperature use'.