Multi-layer 2D material assemblies provide a great number of interfaces beneficial for electromagnetic wave absorption. However, avoiding agglomeration and achieving layer-by-layer ordered intercalation remain challenging. Here, 3D reduced graphene oxide (rGO)/MXene/TiO₂/Fe₂C lightweight porous microspheres with periodical intercalated structures and pronounced interfacial effects were constructed by spray-freeze-drying and microwave irradiation based on the Maxwell–Wagner effect. Such approach reinforced interfacial effects via defects introduction, porous skeleton, multi-layer assembly and multi-component system, leading to synergistic loss mechanisms. The abundant 2D/2D/0D/0D intercalated heterojunctions in the microspheres provide a high density of polarization charges while generating abundant polarization sites, resulting in boosted interfacial polarization, which is verified by CST Microwave Studio simulations. By precisely tuning the 2D nanosheets intercalation in the heterostructures, both the polarization loss and impedance matching improve significantly. At a low filler loading of 5 wt%, the polarization loss rate exceeds 70%, and a minimum reflection loss (RL_min) of −67.4 dB can be achieved. Moreover, radar cross-section simulations further confirm the attenuation ability of the optimized porous microspheres. These results not only provide novel insights into understanding and enhancing interfacial effects, but also constitute an attractive platform for implementing heterointerface engineering based on customized 2D hierarchical architectures.