Based on the structural dynamics optimization theory, a vibration optimization design method of a ship foundation by APDL language is presented in this paper. Structural dynamic optimization design of a ship foundation under the constraint of gross weight of a ship cabin is performed by ANSYS to minimize the vibration of ship hull plating. Optimization shows that the thickness of webs has considerable influence on the vibration isolation performance of ship foundation, while changes of the thickness of base panels and brackets have insignificant influence. Optimal thickness combination of webs, panels and brackets of the foundation is obtained through the optimization. Study also provides reference for practical engineering as well as enriches theories and methodologies of novel vibration isolation for ship foundation design.