Embodiments of methods and systems for wafer bonding alignment compensation are disclosed. The method comprises bonding a first pair of wafers including a first wafer and a second wafer, wherein the first pair of wafers have a plurality of corresponding bonding alignment mark pairs each including a first bonding alignment mark on the first wafer and a second bonding alignment mark on the second wafer; measuring alignment positions of the plurality of bonding alignment mark pairs; determining a mean run-out misalignment between the first pair of wafers using the alignment measurement, wherein the mean run-out misalignment indicates a deformation of at least one of the first pair of wafers; and during bonding of a second pair of wafers, controlling a wafer deformation adjustment module to compensate for the run-out misalignment based on the mean run-out misalignment of the first pair of wafers.