This study investigates the application potential of high-performance lightweight materials in automotive energy-absorbing structures. The crash performance of energy-absorbing boxes with different materials and cross-sectional shapes was first evaluated using the LS-DYNA module in ANSYS Workbench, based on key energy absorption criteria. Subsequently, the low-speed crash characteristics of boxes filled with re-entrant and regular hexagonal polyetheretherketone (PEEK) honeycombs were systematically compared with a baseline hollow design and a conventional aluminum foam-filled structure. The results demonstrate that the regular hexagonal PEEK honeycomb-filled structure exhibits superior overall crashworthiness. It achieved an average crash load of 68.04 kN, which is 18.1% higher than that of the hollow design, while maintaining a lower peak load and enhanced structural stability throughout the crushing process. In contrast, although the aluminum foam filler provided high total energy absorption, it incurred a significant peak load and weight penalty. The findings indicate that the PEEK honeycomb filler offers an excellent balance between lightweight design and crashworthiness, providing a theoretical basis for its engineering application in automotive crash protection systems.