The power flow level difference as reduction evaluation criterions in this paper, according the stacking sequence hypothesis of metal, the material property and layers number as design variable, the corresponding material selection optimization mathematical model of structural dynamic optimization based on metal-composite is established. In the end, taking the steel-composite integrated ships structure mounting as an example, the structural dynamic optimization design with multi-variables, multi- constraints problem is presented, and the optimization problems are solved. Computational results show that, defining the power flow model as objective function, combining the metal-composite material selection optimization method, the ships mounting structure will obtain have excellent vibration control capability. The numerical results show that the optimization method is effective and feasible.