Considering the elastic-plasticity of the structure, the combination of bound-ary element method and finite element method (FEM) is employed to present the calcu-lation method for solving the complex coupled dynamic problem of bubble, elastic-plastic structure and the free surface, and the complete three-dimensional calculation program is developed as well. The error between the calculated result and the experimental re- sult is within 10%. Taking a surface ship for example, the three-dimensional calculation program is extended to engineering filed. By employing the program, the response of the ship under the bubble loading is analyzed. From the stress-time history curves of typical elements of the structure, it can be seen that the pressure reaches its maximum when the bubble collapses and this validates that the pressure generated by the bubble collapse and the jet can cause serious damage on the ship structure. From the dynamic process of the interaction between the three-dimensional bubble and the ship, the low order vertical mode of the ship is provoked and the ship presents whip-shaped motion. And the ship does elevation and subsidence movement with the expansion and shrinkage of the bubble. Some rules and conclusions which can be applied to the engineering problems are obtained from the analysis in this paper.