Lightweight, high-strength and efficient electromagnetic interference shielding materials are in urgent demand for aerospace vehicles such as lunar and Mars rovers. SiC nanowire aerogels exhibit low density, chemical stability, and adjustable dielectric properties, rendering them as ideal candidates for high-performance electromagnetic wave protecting materials. However, developing SiC nanowire aerogels with simultaneous strong mechanical properties and efficient electromagnetic interference shielding performance remains challenging. Herein, a class of strong SiC@carbon nanowire aerogel metamaterials with both mechanical robustness and efficient electromagnetic interference shielding are obtained through microstructure design and compositional optimization. The aerogels with designed meta-structures are fabricated by 3D printing followed with chemical vapor deposition of graphene-like carbon. The optimized compressive strength and Young's modulus of the aerogel metamaterial reach up to 1.581 MPa and 46.230 MPa, respectively, showing an increase of about 50–60 times. It also exhibits an electromagnetic interference shielding effectiveness of 38.39 dB and specific shielding effectiveness of 666.53 dBcm3g−1. These good properties are attributed to the synergistic effects of the hierarchical meta-structure and the SiC@carbon nanowires composite constituents, which provides a feasible pathway toward further design of high-performance electromagnetic interference protection materials.