Combined with simulation calculation and experiment, the damage mechanism of shaped charge warhead with hyperbolic liner and eccentric sub-hemisphere liner on water partitioned structure is studied. The results show that in the process of target penetrating, the penetrator formed by the combined charge liner is separated into multiple segments. The head part of the penetrator forms a cavity path to let the subsequent penetration follow with low resistance. The secondary damage performance of the penetrator formed by the combined charge liner is better than that of the hyperbolic liner. The radial size of the head of the penetrator for the hyperbolic liner increases significantly during the penetration process. Although the energy of the penetrator attenuates faster than that of the combined charge liner, the hole size to the target plate is larger than that of the combined charge liner. The research shows that because of the combined action of penetrator and explosion shock wave, the first target plate is completely broken. Cracks appear near the holes of the second target plate and the third target plate, but the length of the second crack is longer than that of the third one. Because of the significant attenuation of water medium and target plate on penetrator and shock wave, the fourth target plate only has regular circular holes and no obvious cracks.