Abstract: The energetic particle radiation environment in the Jovian radiation belt is much higher than that in the Earth’s orbit in terms of the flux and energy levels. So that an appropriate radiation protection design is essential for the success of the Jovian orbiting mission. In the spacecraft design, multi-layer metallic materials are often adopted for the radiation protection. The protective effect is determined by a combination of the radiation environment, the number and the thickness of layers, and the stacking structure of the layers. Therefore, it is difficult to make a satisfactory scheme merely through numerical analysis methods. In this paper, we combine the genetic algorithm with the MU-LASSIS software and propose a method to determine the best structure of the multilayer shielding to minimize the total ionizing dose. With this method, the optimized shielding structure is obtained under the constraint of the total mass of the structure. The best structure is featured by the high-Z and low-Z materials combined, usually laid in double- or triple-layer, and the high-Z material layer is placed outside. With regard to the equatorial orbiting altitude of 10 R_J and 25 R_J for the periapsis and the apoapsis, respectively, the best protective structure under an areal density of 1 g/cm² is that of a 0.829 mm lead layer combined with a 0.158 mm magnesium layer. The total ionizing dose after the shielding structure is 120.3 krad(Si)/a. Compared with the traditional aluminum shielding structure, about 43.6% of the mass can be reduced. This optimization method may be useful in the radiation protection design of the Jovian exploration missions in the future.