Although megasonic cleaning can remove effectively nano particles in the Cu/low-k interconnection post-Chemical Mechanic Polishing (post-CMP) cleaning, the megasonic energy in cleaning may also cause extensive damage to microstructures. To predict the damage, the structural deformation and the stress distribution of Cu and low-k materials in megasonic cleaning were examined with Finite Element Analysis(FEA). Two-dimensional models were used in analysis of the stress-strain of a typical cell impacted by a caviation bubble in the circulate wiring pattern and all of the simulations were performed with ABAQUS. The results show that the maximum stress is concentrated in the binding area between Cu and low-k, which will result in the delamination of low-k materials. When the line width is 22 nm, the stress and deformation reach the largest values by 1 379 MPa and 3.074 nm respectively. When the line width is more than 22 nm, the max stress and max deformation decrease with increase of Cu line width. The increasing frequency will not change the stress distribution and displacement. The results are in agreement with the defect found in industrial applications.