In order to investigate the effect of combined liner structure on the damage performance of shaped charge warhead, the arbitrary Lagrange-Eulerian fluid-structure coupling algorithm based on LS-DYNA software was used to study the formation of penetrator of single EFP shaped charge warhead and different structural combination of shaped charge warhead, as well as the damage of penetrator to target, after verified the effectiveness of the selected model and material parameters. The results indicate that with the addition of top liner before a single EFP liner, the penetrator with higher head velocity and longer configuration can be formed under the shaped charge. Under the condition that the bottom diameter and height of top liner are 0.2 times the diameter of the charge, when the top cone angle is 30°, the head velocity of the penetrator formed by the combined liner is higher than that formed by other combined liner, and the length of penetrator formed by the combined liner is longer than that formed by other combined liner. However, the diameter of the penetrator formed by the combined liner is the smallest, which is related to the propagation of stress waves in the interior of the liner and whether the microelements around the liner can satisfy the requirement of lengthening the penetrator. The hole aperture and through hole aperture under the penetration of combined liner are positively correlated, the hole aperture and through hole aperture are negatively correlated with the penetration depth under the penetration of combined liner. Under the condition that the bottom diameter and the height of the top liner are 0.2 times the diameter of the charge, the hole aperture of the target under the penetration of the combined liner is not significantly different from that under the penetration of the single EFP liner. The through hole aperture of the target under the penetration of the combined liner is about 0.17~0.2 times of the through hole aperture of the target under the penetration of the single EFP liner. The penetration depth of the target under the penetration of combined liner is about 2.7~3.7 times of the penetration depth of the target under the penetration of single EFP liner. According to the power requirements of warhead, the penetration depth of the target can be increased on the basis of ensuring the hole aperture by adding a proper top liner with a suitable structure.