For the purpose of preventing electromagnetic emission, effective electromagnetic interference shielding materials are actively pursued. In this work, three-dimensional (3D) printing technology was employed to manipulate the honeycomb spacers, which were further assembled into multilayered graphene (GN) film-based sandwich structures. Aiming to tuning the dimensions and shapes of the conductive components in the spacers, various sizes of 3D printed honeycomb frameworks along with different conductive composites were fabricated for understanding the effects of sandwich structures and components on the electromagnetic interference shielding. By tailoring the multiple reflection of conductive interface and absorption of spacer, the as-fabricated electromagnetic interference shielding sandwich structures with a thickness of 2 mm shows considerably high shielding effectiveness (49–54.5 dB) in the X-band. With incorporating the carbon nanotube/plasticine composite into the 3D printed honeycomb structures, the tunable permittivity of the composites and designable structure of 3D printed spacer allow for substantially tuning the electromagnetic interference shielding performance in the sandwich structures. The results exhibit that both spacer thickness and the ratios of carbon nanotube-based plasticine composite to 3D printed honeycomb structures play the critical role in dominating the absorption and reflection effectiveness, suggesting novel strategy for fabricating advanced high-performance electromagnetic interference shielding structures.