This paper proposes using Finite Element Analysis (FEA) simulations to optimize the design structure for low-frequency Magnetically Shielded Rooms (MSRs). In constructing a multi-layer MSR, the different characteristics of the material and laminated structure will bring different levels of magnetic Shielding Effectiveness (SE). The theoretical SE of an MSR can be determined quickly. By using the method used in this paper, the ideal laminated material structure can be found without increasing the MSR construction cost. According to the simulation results and the actual MSR measurement results we built, the optimized MSR design structure can improve the SE by 13 dB. In the area where the external measurement magnetic field is 37 820 nT, the magnetic field in the MSR is as low as 28 nT, and the SE of the MSR is higher than 57.3 dB. The method proposed by this research can provide the theoretical basis for optimal design structure and the FEA simulation method for engineering practice, which can effectively improve the SE of shielded rooms and save the construction cost. The FEA simulations used in this paper can be obtained from the following URL: https://github.com/YuukiAsuna/-Finite-element-simulation-of-material-lamination-sequence .