Abstract Recently, the development of Zn‐host materials in metal‐free aqueous Zinc ion batteries (AZIBs) has emerged as an effective strategy to address the challenges of uncontrollable dendrite growth and severe corrosion in Zn anodes. Herein, the layer‐by‐layer assembly conjugated polyimide nanocomposite (PTN‐MXene) through in situ polymerization is proposed to realize high energy density and stability metal‐free AZIBs. Specifically, the unique layered structure and abundant redox centers of conjugated diketone‐based polyimide (PTN), combined with its high structural compatibility with MXene, enable the formation of a layer‐by‐layer assembled 2D/2D heterostructure. This design ensures sufficient contact and expands the interlayer spacing of MXene, facilitating faster electron/ion transport kinetics and providing better access to redox centers. Importantly, the regulation of ion transport behavior from H + or Zn 2+ to H + /Zn 2+ coinsertion in PTN‐MXene is achieved and verified by different characterization techniques. Thus, PTN‐MXene anode exhibits high specific capacity (283.4 mAh g −1 at 0.1 A g −1 ), excellent rate performance and outstanding cycling performance. As a proof‐of‐concept, the full batteries fabricated by Prussian blue analogs cathode and PTN‐MXene anode deliver a high energy density of 72.4 Wh kg −1 and exceptional cycling stability over 2000 cycles.