A wet model topology optimization method based on added mass method and bidirectional evolutionary structure optimization algorithm is proposed to maximize the natural frequency of fluid-structure coupling system. The fluid-structure coupling equation of the finite element method and the sensitivity formula of the element are analyzed simultaneously, and then the coupling optimization model is established. Under the constraints of structure volume, the weighted natural frequencies of single-objective and multi-objective of the coupled system are maximized to optimize the underwater coupled structure. The numerical results show that the evolutionary methods can be applied to this kind of problem effectively and efficiently. Besides, the optimization results of cases have smooth boundaries and the numerical stability of the optimization algorithm is good. Under constant volume constraints, the single-order natural frequency is increased by more than 380%. The results of multi-objective weighted optimization show that the weighted coefficients are final. The larger the weighting coefficient is, the closer the topological form is to the optimal result of the model.