To study the charge damage evolution process when a high-velocity warhead penetrated a double-layer target, a numerical simulation study was conducted using a cohesive zone model to investigate the penetration of double-layer target. The cohesive zone model was utilized to calculate the occurrence and evolution of PBX damage, as well as to analyze the relationship between the penetration velocity and damage evolution. The quantification of damage was conducted by means of the damage ratio. Furthermore, a micro-damage finite element model for PBX was established to examine the microscopic damage mechanisms during penetration into a double-layer target. The results show that when the projectile penetrates the target plate vertically, the extent of damage of the charge increases with the increase of penetration velocity. From a microscopic perspective, it was observed that cyclic tensile and compressive loads induced the formation of vertical cracks perpendicular to the loading direction. The primary mechanism of damage in PBX charge penetration into double-layer target is interface debonding. Additionally, the microcracks destabilize, propagate, and converge into a continuous main crack.