The self-assembled three dimensional (3D) hybrids nanostructure containing uniform growth of vertical carbon nanotubes (VCNTs) with faceted iron oxide nanoparticles (f-Fe3O4 NPs) on the surfaces of reduced graphene oxide nanosheets (rGO NSs) is achieved using microwave assisted approach. The formation of hierarchical 3D f-Fe3O4-VCNTs@rGO hybrids, using microwave method is a rapid, simple, and inexpensive synthetic route. First, the VCNTs grow with help of Fe NPs, and after oxidizing of Fe NPs in form of f-Fe3O4 NPs, the growth has terminated resulting in formation of small size (<500 nm) VCNTs containing f-Fe3O4 NPs on its tip. The defect- and oxygen-rich sites of rGO NSs favor the heterogeneous nucleation and growth of f-Fe3O4 NPs on the tip of VCNTs. The synthesized 3D f-Fe3O4-VCNTs@rGO hybrid shows the improved electromagnetic interference (EMI) for microwave shielding effectiveness (SE) as compared to both rGO NSs and Fe3O4 NPs@rGO NSs materials. This 3D f-Fe3O4-VCNTs@rGO hybrid demonstrates the shielding effectiveness value more than ∼25 dB as compared to Fe3O4 NPs@rGO NSs for 1.0 mm thin film of 3D f-Fe3O4-VCNTs@rGO hybrids in microwave X-band (8.2–12.4 GHz). This applied microwave synthesis approach for 3D f-Fe3O4-VCNTs@rGO hybrids is simple, fast, reproducible and scalable for advanced EMI shielding materials. It can be concluded that the faceted Fe3O4 NPs on the tip of VCNTs which are grown in-situ on rGO NSs shows synergetic performance for EMI shielding elements in advanced application areas like spacecraft and aircraft.