Semiconductor performance is required to continually improve as technology advances. Specifically, 3D stacked IC technology is becoming increasingly important in meeting these demands. In this study, we investigate the effect of the device structure on the post-bonding distortion, which causes a misalignment of the Cu-Cu pad resulting in electrical conduction failure. To understand this, we built a simulation model that incorporates the deflection of two bonded wafers and the air resistance caused by fluid flow dynamics between the wafers. We found that the density distribution of the Cu-Cu pad affects the bonding wave propagation velocity in each direction and changes the shape of the bonding front and post-bonding distortion. The result is a change in the Cu-Cu pad misalignment.