The study aims to improve the damage resistance of high-strength concrete (HSC) under penetration by applying the multilayer concept. The designed layered HSC consists of three layers, i.e., crack-resistant layers at the top and bottom of the sample (concentrating steel fibers), and a penetration-resistant layer in the middle (containing coarse basalt aggregates). A series of penetration experiments were carried out and influencing factors such as aggregate size and fiber shape were discussed. The study reveals that the designed layered HSC provides superior damage resistance compared to the single-layered reference HSC, with a 66% reduction in the crater diameter and a crater volume about 13% of that of the reference group. The improved damage resistance of the layered HSC is associated with the synergistic effect of the aggregate size and the fibers shape. It is exhibited that straight fibers produce smaller crater sizes when the penetration-resistant layer consists of smaller aggregates, i.e., 10 mm to 30 mm; conversely, hooked-end fibers produce better damage resistance when the aggregate size is between 50 mm and 80 mm. The results of this study contribute to the understanding of the ballistic properties of layered HSC, and promote its application in protective structures.