Synchronous manipulation of meso-structure and architecture of covalent organic frameworks (COFs) is vital for customized applications but still remains challenging. Here, we develop a polymerization-induced co-assembly approach to construct hierarchical porous COF-based nanosheets with adjustable large mesopores (7–40 nm), intrinsic micropores (∼1.2 nm), ultra-thin thickness (∼24 nm), and a crystalline wall. Furthermore, density functional theory calculations and adsorption experiments indicated that the complementarity of the two-dimensional architecture and intrinsic micropores of COFs can effectively confine iodine molecules. Meanwhile, the exposed nitrogen-containing active sites created by the unique mesoporous structure can strongly anchor iodine species, thereby greatly inhibiting their dissolution and shuttling. Therefore, as a cathode for zinc-iodine battery, they delivered an outstanding rate capability (191.2 mAh g−1 at 0.5 A g−1) and stable long-term cyclability (154.8 mAh g−1 at 3 A g−1 after 20,000 cycles). This approach sheds light on the precise fabrication of crystalline porous materials for diverse applications.