To improve the shielding performance of a multilayer magnetically shielded structure and to further reduce the construction cost of a magnetically shielded room， this study proposes to treat the magnetically shielded structure as a multi-objective function optimization problem， and to optimize the parameters of the shielded lamination structure using the non-dominated sorting genetic algorithm-II （NSGAII） under the constraints of feasible construction cost and quality construction composition. In this study， the NSGAII algorithm is improved using a segmental crossover strategy with an adaptive variation operator called CSA-NSGAII to solve the problems of the traditional NSGAII algorithm of uneven population convergence distribution， poor global search ability， and easily falling into a local optimum. Compared with the original NSGAII algorithm， NSGAII-SDR， g-NSGAII， and MOEA/D algorithms， the CSA-NSGAII is beneficial in GD， IGD， and spacing， indicating that the proposed CSA-NSGAII algorithm achieves improved convergence performance and a more uniform population distribution. By applying the algorithm proposed in this paper to the multi-objective optimization design problem of the magnetic shielding structure， the experimental results show that the optimized stacked structure can， on average， save approximately 14% of the construction costs while achieving the same shielding performance， and can achieve approximately 70 dB of shielding performance in a Helmholtz coil with an interference amplitude of 32 000 nT and frequency of 1 Hz.