Robust, ultra-flexible, and multifunctional MXene-based electromagnetic interference (EMI) shielding nanocomposite films exhibit enormous potential for applications in artificial intelligence, wireless telecommunication, and portable/wearable electronic equipment. In this work, a nacre-inspired multifunctional heterocyclic aramid (HA)/MXene@polypyrrole (PPy) (HMP) nanocomposite paper with large-scale, high strength, super toughness, and excellent tolerance to complex conditions is fabricated through the strategy of HA/MXene hydrogel template-assisted in-situ assembly of PPy. Benefiting from the "brick-and-mortar" layered structure and the strong hydrogen-bonding interactions among MXene, HA, and PPy, the paper exhibits remarkable mechanical performances, including high tensile strength (309.7 MPa), outstanding toughness (57.6 MJ m−3), exceptional foldability, and structural stability against ultrasonication. By using the template effect of HA/MXene to guide the assembly of conductive polymers, the synthesized paper obtains excellent electronic conductivity. More importantly, the highly continuous conductive path enables the nanocomposite paper to achieve a splendid EMI shielding effectiveness (EMI SE) of 54.1 dB at an ultra-thin thickness (25.4 μm) and a high specific EMI SE of 17,204.7 dB cm2 g−1. In addition, the papers also have excellent applications in electromagnetic protection, electro-/photothermal de-icing, thermal therapy, and fire safety. These findings broaden the ideas for developing high-performance and multifunctional MXene-based films with enormous application potential in EMI shielding and thermal management.