Developing materials that possess high electromagnetic interference (EMI) shielding capability, as well as flexibility and lightweight characteristics is a persistent challenge. To address this issue, an ultra-flexible heterogeneous composite film composed of hollow-Fe3O4@MXene, silver nanowires (AgNW), and high-strength bacterial cellulose (BC) is developed via a vacuum-filtration method. The hollow-Fe3O4@MXene hybrids integrate magnetic loss from Fe3O4 and electrical loss from MXene, while the AgNW form a conductive network that enhances the absorption and reflection of electromagnetic waves (EMWs). BC is a biocompatible and flexible matrix that ensures mechanical robustness. The hollow-Fe3O4@MXene/AgNW/BC (H-Fe3O4@M/Ag/BC) composite film exhibits outstanding EMI shielding effectiveness (SE), reaching 59 dB in the X-band, which is attributed to the synergistic effects of multiple interfacial polarizations, conductive loss, and magnetic loss in the heterogeneous structure. The film also demonstrates excellent flexibility and mechanical strength (as high as 12.1 Mpa), making it suitable for use in flexible electronic devices. The film also exhibits excellent hydrophobic, flame-retardant, infrared stealth, thermoelectric, and photothermal conversion properties. This study provides a novel strategy for designing high-performance EMI shielding materials with integrated functionality and flexibility.