Ensuring effective energy absorption is especially critical for crewed missions and biological payloads. This study aims to design and evaluate a three-dimensional (3D) metamaterial structure, derived from a two-dimensional (2D) re-entrant unit cell, as an efficient energy absorber during the landing phase of space missions. The primary objective is to develop a lightweight structure with enhanced energy absorption capacity, suitable for integration into space systems. A novel 3D cylindrical metamaterial was developed by rotating 2D re-entrant unit cells around a central vertical axis. Two materials were used for sample fabrication: thermoplastic polyurethane (TPU) for the 2D structures and polylactic acid (PLA) for the 3D structures. All samples were produced using fused filament fabrication (FFF) 3D printing technology. Quasi-static compression tests were performed on the 3D samples to assess their mechanical behavior and energy absorption performance. Force-displacement data were recorded and analyzed to determine the energy absorption metrics. The 3D metamaterial structure demonstrated superior energy absorption capabilities. It was able to absorb a total of 148.39 J of energy and exhibited a specific energy absorption (SEA) of 2.232 kJ/kg. These values significantly surpass those reported in previous studies for comparable structures, indicating the effectiveness of the new design. The proposed 3D metamaterial structure, fabricated via FFF 3D printing and based on a rotated re-entrant unit cell design, exhibits excellent energy absorption performance. Its high SEA and lightweight configuration make it a strong candidate for use in the impact mitigation systems of space payloads, offering promising potential for future space applications.