The lightweight of rack EMU（Electric Multiple Units）body is one of the key factors to realize the strong climbing ability and comfort of rack EMU. Aiming at the lightweight design of rack EMU body floor beam, a structural design method combining 2 D with 3 D based on modal analysis and topology optimization theory was proposed. Firstly, the topology optimization of the 2 D section of floor beam with the minimum strain energy was carried out by using the finite element analysis and the structural optimization design software, and the topology configuration of the coarse section was obtained. Then, based on the coarse topological configuration, the multi-objective topology optimization of strain energy minimization and modal maximization for the 3 D structure of floor beam were carried out to obtain the 3 D structure shape of floor beam containing modal factors. Finally, the new configuration suitable for the rack-rail floor beam section was constructed based on the two optimization results and the manufacturability of floor beam, and the finite element simulation results were compared, analyzed and verified under the same boundary conditions as the original structure. The results show that the strength, stiffness and modal performance of the configuration satisfy with the requirements of the rack EMU body, and the quality of the optimized structure is 6.835% lower than the original structure.