The bonding of glass wafer to aluminum foils in multi-layer assemblies was made by the common anodic bonding process. The bonding was performed at temperatures in the range 350-450 °C and with an applied voltage in the range 400-700 V under a pressure of 0.05 MPa. Residual stress and deformation in samples of two-layer (aluminum/glass) and three-layer (glass/aluminum/glass) were analyzed by nonlinear finite element simulation software MARC. The stress and strain varying with cooling time were obtained. The analyzed results show that deformation of the three-layer sample is significantly smaller than that of the two-layer sample, because of the symmetric structure of the three-layer sample. This has an important advantage in MEMS fabrication. The maximum equivalent stresses locate in the transition layer in both samples, which will become weakness in bonded sample.