The LS-DYNA simulation software was used to study the overload characteristics of a projectile penetrating a layered protective structure at high velocity. Firstly, the simulation data were compared with experimental data to verify the accuracy of the finite element model. The process of projectiles penetrating two different protective structures was analyzed, and the overload characteristics of the projectile under different working conditions were studied. Results show that the peak overload of the projectile penetrating the light protective structure at 1200 m/s and 1700 m/s can exceed 80,000 g and 130,000 g, respectively, and the peak overload of the projectile penetrating the heavy protective structure at 1200 m/s and 1700 m/s can exceed 40,000 g and 70,000 g, respectively. When the projectile penetrates a lightweight protective structure with different material shielding layers at the same velocity, the overload peak value of penetrating the shielding layer material of reinforced concrete is greater than that of penetrating the shielding layer material of granite. The deceleration peak value of the projectile penetrating a light protective structure is larger than that of a projectile penetrating a heavy protective structure at the same velocity mainly due to the good buffering effect of the thick soil layer of the heavy protective structure.