The purpose of this study is to perform an analysis of the structure stability of a breakwater concerning the effect of wave overtopping. First, a COBRAS model of Taichung Harbor breakwater structure is created. Secondly, the model is verified with experimental data, and reasonable agreement is shown between the two. Finally, the breakwater stability analysis under 50 to 250-year-return-period typhoon wave conditions as well as extreme wave conditions is discussed. The result shows that the failure of sliding is more dangerous than the failure of overturning in Taichung harbor breakwater. Under the extreme wave more than 100 year-return-period, the breakwater is unstable in sliding, whereas that is safe in overturning. The influence of Wave Overtopping on the Stability Analysis is dominated by the force on rear side of caisson and the phase difference on the two ends of caisson. If the impulse force happens at the moment of the minimum of the front force, the safety factor might decrease significantly and the failure of sliding might cause breakwater damage.