• • Single-crystal structures of five binodal [4+4] 2D COFs (NKCOF-88 to -92) were solved via 3D electron diffraction at resolutions of 0.90–1.02 Å, providing atomic-level evidence that all adopt inclined staggered AB stacking, not the assumed AA stacking.
• • The topology-derived synthetic route, based on substituting four-connected nodes with extended monomers decomposable into two three-connected nodes, yields pseudo-bex and pseudo-hcb networks, enabling predictable synthesis of binodal COFs.
• • Linkage conformation (cis+cis, trans+trans, or mixed) directly controls layer geometry: planar layers for uniform alignment, undulated layers for mixed alignment, as confirmed by single-crystal analysis.
• • The inclined AB stacking modes are categorized into three types based on monomer geometry: horizontal (pyrene-based, NKCOF-90/92), diagonal (tetraphenylethylene or terphenyl, NKCOF-88/89), and vertical (NKCOF-91), with edge-to-face π–π interactions stabilizing the structures.