The increasing concern over electromagnetic wave (EMW) contamination has led to the emergence of the EMW-absorbing superstructure element. Cementitious composites typically possess poor electromagnetic wave reflectivity, but this was improved through 3D printing technology, which offers greater productivity and design flexibility. In this study, a new wave-shaped EMW absorbing superstructure was manufactured using 3D cement printing, and mechanical testing showed a significant improvement in flexural and shearing strength. Molecular dynamic simulation was utilized to investigate the mechanism of the enhanced mechanical properties at the molecular scale. The EMW absorption performance of the printed specimens was analyzed from 1 GHz to 18 GHz through the Naval Research Laboratory (NRL) equipment, exhibiting a significant improvement in reflectance, especially in the low-frequency domain. Based on experimental results, the optimized design of the superstructure was proposed, which possesses an average reflection loss of −25 dB, a peak reflectivity of −37.4 dB, and an absorbing bandwidth of 17 GHz. These findings suggest that the 3D-printed EMW absorber element has great potential for use in minimizing electromagnetic contamination in various applications.