On the background of development of wafer level package (WLP) of inertial MEMS devices, further miniaturization of inertial system is promoted by 2.5D/3D integration technology. This paper evaluates the impact of 3D stack technique on the output performance of stress sensitive MEMS devices. By optimization of 3D interconnection structure distribution and increasing substrate thickness, the thermal deformation and bending is decreased to about 8nm and 4nm, respectively. Finally, 3D integration of MEMS sensor with air-gapped Si-TSV and the ASIC is verified with relatively low stress Si-TSV based interposer. The proposed 3D integration design is suitable for 3D integration of MEMS inertial sensors dies and ICs dies.