Honeycomb sandwich (HS) structures are important lightweight and load-bearing materials used in the aerospace industry. In this study, novel honeycomb-hollow pyramid sandwich (HPS) structures were manufactured with the help of fused deposition modeling techniques using PLA and PLA/CNT filaments. The microwave and mechanical energy absorption properties of the HPS structures with different geometry parameters were studied. Compared with the HS structure, the HPS structure enhanced both microwave absorption and mechanical properties. The HPS structures possessed both broadband and wide-angle microwave absorption characteristics. Their reflection loss at 8-18 GHz for incident angles of up to 45° was less than -10 dB. As the thickness of the hollow pyramid increased from 1.00 mm to 5.00 mm, the compressive strength of the HPS structure increased from 4.8 MPa to 12.5 MPa, while mechanical energy absorption per volume increased from 2639 KJ/m to 5598 KJ/m . The microwave absorption and compressive behaviors of the HPS structures were studied.