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Nowadays, three-dimensional (3D) integration has been widely applied in semiconductor and electronics industry. When 3D integration applied in MEMS (micro electromechanical system) packaging, it is possible to stack host MEMS chip/wafer with other chips/wafers (such as ASIC) to lower package profile and realize area array sensor system. In this paper, a miniaturized piezoresistive pressure sensor system with TSV structure has been designed to demonstrate the application of TSV in MEMS packaging. TSV in pressure sensor chip is designed to provide communication paths for electrical signals. Cu/Sn bump is electroplated after exposing TSV from backside and backside metallurgy. Signal read-out chip contains redistribution circuits and Au studs. The pressure sensor chip and signal read-out chip are flip chip bonded using Au-Sn eutectic bonding. To realize this pressure sensor system, a systematic process flow including piezoresistors fabrication and circuits patterning, TSV process, flip chip bonding, polymer hermetic sealing is designed and implemented experimentally.