The purpose of this study is to perform the stability analysis of breakwater, concerning the overtopping effect. First, a COBRAS model of the 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, concerning the overtopping effect, under 50 to 250-year return-period typhoon wave conditions as well as extreme wave conditions is discussed. The result shows that the overtopping effect will cause the sliding safety factor and overturning safety factor to oscillate.