Shaped charge warhead which is widely utilized for underwater weapons has a severe threat to the survivability of naval ships. Therefore, it is of great significance to improve their anti-destructive capability. Three types of loads - shock wave (SW), shaped charge projectile (SCP) and bubble - are generated during the process of shaped charge associated with underwater explosion, which can cause different damage characteristics into double-hull structure. In this paper, these three loads characteristics and their combined damage into double-hull structure are analyzed. Besides, the protection of fiber metal laminates on this structure are discussed. Firstly, Coupled Eulerian-Lagrangian (CEL) is used to simulate the full physical process of double-hull subjected to shaped charge associated with underwater explosion. Secondly, the damage characteristics of double-hull are obtained under the combined damage of the shock wave, shaped charge projectile and bubble. After that, the steel plate/UHMW-PE laminate (Fiber Metal Laminate, FML) is designed according to the equal surface density theory. The blast and penetration resistance of ultra-high molecular weight polyethylene (UHMW-PE) material is analyzed and the optimized FML models are discussed. The results show that a small plastic deformation and hole of the outer and inner plates of the double-hull are generated by the shock wave and the shaped charge projectile, respectively. A large plastic deformation of the outer plate is caused by the subsequent bubble load, which is torn and pulled off. The hole size of plate coated with PE and the residual velocity of projectile reduced by 26.66% and 69.50% compared with those of the steel plate, respectively. Besides, for the coated cases the outer and inner plates is respectively not pulled off and penetrated by projectile. Additionally, it is worth noting that the bubble collapses and cannot cause the secondary damage into double-hull due to the protection of coated PE. It indicates that the PE has a great protection performance of the double-hull subjected to shock wave, bubble and projectile, which can provide a reference for the naval ships protection design.