An interconnection structure of a system on wafer and a PCB based on a TSV process and a method for manufacturing the same. The structure comprises a bottom structural part and a top structural part, the upper surface of the bottom structural part is provided with a plurality of positioning holes; the lower surface of the top structural part is provided with positioning pins; the upper surface of the bottom structural part is provided with a bottom groove, and a system on wafer is arranged in the bottom groove; the lower surface of the system on wafer is connected with the bottom groove; the lower surface of the top structural part is provided with a top groove, and a PCB preformed die is connected in the top groove, and the other end of the PCB preformed die is connected with the system on wafer by an elastic connector.