Silicon-glass bonding technology is critical to the development of durable micro-inertial devices. Because the thermal expansion coefficients of silicon and glass are different, thermal stress is produced on the silicon-glass contact surface when the operating temperature of the inertial device changes.This can have a serious effect on the performance of the device. Therefore, an understanding of the extent of thermal mismatch stress between these heterogeneous materials and the effect of bonding anchor point size on stress are important for the improvement of the structure and process design of these devices. In this paper, a method of anchor deformation measurement and data processing using a cantilever beam as the test structure is proposed to characterize the process thermal mismatch stress of the device. The simulation results indicate that anchor points designed in block form reduce the maximum stress and structural deformation. For anchor points with side lengths of 600 μm, 400 μm, and 200 μm, the average off-plane displacements of the cantilever beam relative to the anchor points are 0.43 nm/℃, 0.30 nm/℃ and 0.20 nm/℃, respectively. These results have good repeatability. Our results show that the thermal deformation of anchor points is directly related to the size of the anchor points, and this has important research significance for the improvement of MEMS inertial structure and process design.