Magnetic Fe3O4 nanoparticles were deposited on the high-performance bacterial cellulose (BC) by the in-situ co-precipitation. Subsequently, the magnetic and conductive BC@Fe3O4/AgNWs composite films with hierarchical structures were successfully prepared via the two-step vacuum assisted filtration method. The microstructures and properties were analyzed by scanning electron microscopy (SEM), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD) and vector network analyzer. The results show that when the AgNWs area fraction is 1.8 g/m2, the electromagnetic interference shielding effectiveness (EMI SE) of the composite films can reach 56 dB. Moreover, there is a good interface interaction between the AgNWs and BC@Fe3O4 matrix, thus leading to the excellent mechanical properties of BC@Fe3O4/AgNWs composite films. The maximum tensile strength and elongation at break are 84.6 MPa and 4.05%, respectively. The resultant flexible, mechanically strong and high EMI SE bacterial cellulose-based composite films have good application prospects in the fields of flexible wearable electronic devices.