Ultrathin (∼2 μm) reduced graphene oxide (rGO) film embedded with self-aligned Fe3O4 nanodiscs were successfully fabricated through the filtration-assisted self-assembly method. In the as-fabricated hybrid film, Fe3O4 nanodiscs with thin thickness (26 nm) and high aspect ratio (∼9) were readily self-assembled and aligned in rGO intersheets under the assistance of hydrostatic forces. Compared with spherical Fe3O4 nanoparticles, introducing the Fe3O4 nanodiscs into rGO paper could not only offer high magnetic permeability and magnetic loss in a broad frequency range at the gigahertz level, but also increase the electrical conductivity of rGO film by means of improving the surface roughness without disrupting the conductive network of the rGO layers. Due to the above advantages, the free-standing rGO/Fe3O4 nanodisc magnetic hybrid film (56 wt%) exhibited an EMI shielding effectiveness (SE) of around 11.2 dB in the frequency range of 2-10 GHz, which is about 50% and 72% higher than that of neat rGO film and rGO/Fe3O4 nanosphere hybrid films (with similar particle size and loading weight fraction) prepared under the same conditions, respectively. Furthermore, compared with non-magnetic neat rGO film, the outstanding magnetic properties of the rGO/Fe3O4 nanodisc film paves the way for it to be used as a multifunctional material that can be controlled by magnetic fields. Additionally, the moderate thermal reduction temperature (420 °C) would be meaningful for large scale fabrication. Meanwhile, the strategy of achieving good alignment at the nanoscale could shed light on developing heterogeneous structures with self-aligned two-dimensional (2D) (magnetic or non-magnetic) nano-inclusions for various applications.