There has been an urgent need to develop and analyse multi-layered composite structures with varying material properties to withstand projectile impact. The proposed study focuses on the optimization of the multi-layer composite to achieve maximum resistance/energy dissipation. This study investigates the mechanical performance of the proposed multi-layered composite configuration under high strain rate loading through a computational approach. The proposed multi-layered structure incorporates layers of reinforced concrete, boulders, an elastomer layer, an ultra-high-performance concrete panel, and a layer of steel plate. A mesoscale-based approach has been developed for the layer comprising boulders and mortar. A total of six different configurations have been considered to arrive at the most efficient one against projectile impact. Optimization of the proposed configurations has been done by utilizing the concepts of specific energy absorption and shock impedance. Additionally, the fracture and damage characteristics of each configuration are also studied. Ductile hole enlargement in the sandy soil layer, fragmentation failure in the boulders, petaling failure in the steel plate, and spalling failure in the concrete layer have been observed. Based on the specific energy absorption and shock impedance approaches, the optimum laying sequence for the ballistic impact of each material is suggested.