The vibration power flow level varying of a structure was taken as a vibration reduction evaluation criterion here. Based on the metal stacking sequence hypothesis, the material property and layer number were taken as design variables, a structural dynamic optimization model based on metal-composite material selection optimization was established. Taking a steel-composite integrated ship's structure mounting as an example, the structural dynamic optimization design with multi-variable and multi-constraint was conducted, and the optimization problem was solved. Computational results showed that taking the vibration power flow as an objective, combining the metal-composite material selection optimization method, the ship's mounting structure can have an excellent vibration-suppressing capability, the proposed optimization method is effective and feasible.