Developing ultrathin electromagnetic interference (EMI) shielding materials with high-efficiency EMI shielding effectiveness (SE), anisotropic thermal conductivity and robust mechanical performance is urgently required but challenging to satisfy the integration and miniaturization of modern flexible electronics. Herein, an alternating multilayered film containing alternating CoFe₂O₄@MXene/cellulose nanofibers (CNF) layers and silver nanowires (AgNWs)/CNF layers was successfully fabricated via a facile alternating vacuum-assisted filtration strategy. Profiting from the rational arrangement of CoFe₂O₄@MXene/CNF layers and AgNWs/CNF layers, electric/ magnetic coupling effect and unique “absorption-reflection-reabsorption” shielding behavior among the alternating multilayered films, the resultant composite film with alternating six-layered architecture realizes an ultrahigh EMI SE of 87.8 dB with low electromagnetic waves reflection effectiveness of 5.6 dB at a thickness of only 0.1 mm. The film remains reliable EMI shielding performance (over 97% EMI SE retention) after undergoing persistently physical damage and prolonged chemical attack. Meanwhile, owing to the construction of overlapping AgNWs network, the obtained film acquires outstanding in-plane thermal conductivity (6.875 W/(m·K)) and controllable Joule heating performance (steady temperature over 90 ?C at applied voltage of 3.0 V within 20 s). The inferior through-plane thermal conductivity (0.689 W/(m·K)) caused by the design of multilayered structure guarantees the remarkable infrared stealth performance. Additionally, the good interfacial interaction endows the prepared film with robust mechanical properties (tensile strength of 183.2 MPa and fracture strain of 5.4%). This work not only offers a creative avenue for designing and preparing multifunctional EMI shielding composite films with excellent mechanical properties, but also broadens the applications of EMI shielding composite films in military fields, artificial intelligence and wearable electronics.