We present a new double-sided, single-chip monolithic integration scheme to integrate the CMOS circuits and MEMS structures by using through-silicon-via (TSV). Neural sensing applications were chosen as the implementation example. The proposed heterogeneous device integrates standard 0.18 μm CMOS technology, TSV and neural probe array into a compact single chip device. The neural probe array on the back-side of the chip is connected to the CMOS circuits on the front-side of the chip by using low-parasitic TSVs through the chip. Successful fabrication results and detailed characterization demonstrate the feasibility and performance of the neural probe array, TSV and readout circuitry. The fabricated device is 5 × 5 mm2 in area, with 16 channels of 150 μm-in-length neural probe array on the back-side, 200 μm-deep TSV through the chip and CMOS circuits on the front-side. Each channel consists of a 5 × 6 probe array, 3 × 14 TSV array and a differential-difference amplifier (DDA) based analog front-end circuitry with 1.8 V supply, 21.88 μW power consumption, 108 dB CMRR and 2.56 μVrms input referred noise. In-vivo long term implantation demonstrated the feasibility of presented integration scheme after 7 and 58 days of implantation. We expect the conceptual realization can be extended for higher density recording array by using the proposed method.