Missile electromagnetic launching technology is a new type of launching technology. During the launching of the missile, a strong electromagnetic environment was produced, which would not only seriously interfere with the normal operation of electronic components in the missile, but also destroy the external electromagnetic environment and affect the other equipment. Therefore, taking certain electromagnetic shielding measures was very important for the launching process. In this paper, the multi population genetic algorithm (MPGA) was combined with the design of multi layers material shielding to make simulation. The results showed that, compared with standard genetic algorithm, the shielding effectiveness of the shield design based on multi population genetic algorithm was higher, and the optimization results were more stable and efficient. So the multi population genetic algorithm will achieve better shielding effectiveness in the missile electromagnetic launching process.