A 3D system-level packaging method includes providing a packaging substrate having a first functional surface and a second surface with wiring arrangement within the packaging substrate and between the first functional surface and the second surface. The method also includes forming at least one flip package layer on the first functional surface of the packaging substrate and forming at least one wiring and package layer on the flip package layer. The flip package layer is formed by subsequently forming a flip mounting layer, an underfill, a sealant layer, and a wiring layer; and the wiring and package layer is formed by subsequently forming a straight mounting layer, a sealant layer, and a wiring layer. Further, the method includes planting connection balls on the second functional surface of the packaging substrate.