A numerical model of a Nextel/Kevlar-filled protective structure under hypervelocity impact is developed to investigate its structural response and optimize its configuration. Four key design parameters, namely the thicknesses of the front plate, Nextel and Kevlar layers, and rear plate, are chosen as variables. Latin hypercube sampling is employed to generate sample points, and high-fidelity simulations are carried out using LS-DYNA to obtain the projectile’s kinetic energy dissipation. A Kriging surrogate model is built to approximate the simulation response with reduced computational cost. Based on the surrogate, a multi-objective optimization using the NSGA-II algorithm is performed, aiming to minimize the areal density and maximize energy dissipation. The optimized structure achieves a 2.56% reduction in areal density and a 1.91% increase in energy loss.