Long-span structure is one of the typical structure features of ships. Low rigidity of the long-span structure causes large structure displacement and vibration amplitude, imposing difficulties in the vibration reduction design. The vibration of the long-span grillage structure is analyzed for a ship under bow thruster excitation in the current study. Topology optimization base structure is then established for the arrangement of the pillar under the long-span grillage structure. With the objective function of lightest structure weight based on SIMP method, the dynamic topology optimization design is carried out by using the stand pillar arrangement topology optimization model considering the vibration velocities of specified nodes as the constrain. The results show that a pillar arrangement plan with good vibration control performance is obtained by using the long-span pillar topology optimization method in the current study. This method can reduce the complexity of the design and the workload of the dynamic calculation, with a better vibration damping effect.