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The article relates to the fabrication of embedded P-N junction capacitors, using System-in-Package (SiP) technology, on a silicon interposer wafer with Through-Silicon-Via (TSV). The P-N junction capacitors are fabricated using current micromachining technologies, including etching high aspect-ratio, three-dimensional honeycomb structure and thermal oxidation, thermal dopant diffusion, sputtering, and metallization and so on. The fabricated capacitor displays high capacitance density compared with common two-dimensional (2D) P-N junction capacitors. Tests at high frequency (10 Mhz-40 GHz) were conducted to evaluate the properties of these capacitors. Test results show that the capacitors have a high capacitance density up to 12 nF/mm2 of wafer area, with reverse bias voltage of 1 V, which is about 10-12 times that of 2D semiconductor capacitors, and is attributed to the increased junction area inherent in the three-dimensional via structure. These capacitors can be used for decoupling under a wide frequency range from 300 MHz to 3.2 GHz. they show a low parasitic inductance by measuring. Capacitor has a characteristic that capacitance value also keeps up constant with the increase of frequency.