This paper examines the response characteristics of a warship’s double-layer plates under a secondary near-field explosion after the ship’s outer plate has been perforated by shaped metal jets. First, the effectiveness of the Coupled Eulerian–Lagrangian (CEL) method was validated, showing numerical simulations to be well aligned with experimental results. Subsequently, the damage inflicted on the outer plate by metal jets was simplified to a prefabricated orifice, further studying the explosive impact response of double-layer plates under different inter-compartmental water levels and charge distances. Our findings indicated the following: (1) shockwave and bubble pulsation loads are the main causes of deformation in the outer plate; (2) the driving of the outer plate and the flooding water between compartments are the main causes of deformation in the inner plate; and (3) deformation in the outer plate will decrease as the water level in the compartment increases, while deformation in the inner plate will increase with the increasing water level. Consequently, under certain specific damage, the ingress of water into a compartment effectively enhances the explosion resistance of the double-layer plates.