In recent years, the design of energy-absorbing structures with negative Poisson’s ratio (NPR) has gained considerable attention due to their superior mechanical performance under dynamic and quasi-static loads. However, conventional auxetic structures often suffer from limited energy absorption capacity and structural instability at large deformations. This study introduces a novel hierarchical re-entrant lattice metastructure, fabricated using material extrusion by fused filament fabrication (FFF) 3D printing, to overcome these limitations. The research methodology involved designing both conventional and hierarchical 3D auxetic structures, characterizing their mechanical properties through quasi-static compression tests, and validating the results using finite element analysis. Key performance metrics such as specific energy absorption (SEA), peak force, mean crushing force, and crush force efficiency were evaluated. Finite element analysis show that the hierarchical design significantly enhances energy absorption capabilities. The hierarchical 3D structure absorbed energy 295% more than its conventional counterpart and its SEA represents a 144% improvement. Although the conventional design exhibited higher crush force efficiency, the hierarchical structure demonstrated superior overall performance. The proposed hierarchical auxetic metastructure offers a promising solution for advanced energy-absorbing applications, particularly in aerospace and protective systems, where lightweight and high-performance materials are essential.