The invention relates to a method for manufacturing a three-dimensional packaging structure of double-faced SiP. The method comprises the following steps: step 1, taking a temporary support plate; step 2, laminating a core transfer plate on the temporary support plate; step 3, laminating a fan-shaped wafer level packaging structure, a first passive element and a first 3D conducting part on the front face of the core transfer plate; step 4, performing plastic package work; step 5, performing mechanical grinding to expose the first 3D conducting part, and removing the temporary support plate; step 6, laminating a chip, a second passive element and a second 3D conducting part on the back face of the core transfer plate; step 7, performing plastic package and ball implanting work; and step 8,performing next step packaging process or cutting to form single products, and accomplishing the test. By adoption of the method, a prefabricated 3D conducting part with a small center distance can beused as the supporting structure of stacking and packaging, the height of the packaging module can be reduced, the high-frequency performance, and the height design and tiling control flexibility ofthe packaging module can be improved.