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Crystalline porous covalent frameworks (COFs) have been considered as a platform for uranium extraction from seawater and nuclear waste. However, the role of rigid skeleton and atomically precise structures of COFs is often ignored in the design of defined binding configuration. Here, a COF with an optimized relative position of two bidentate ligands realizes full potential in uranium extraction. Compared with the para-chelating groups, the optimized ortho-chelating groups with oriented adjacent phenolic hydroxyl groups on the rigid skeleton endow an additional uranyl binding site, thereby increasing the total number of binding sites up to 150%. Experimental and theoretical results indicate that the uranyl capture is greatly improved via the energetically favored multi-site configuration and the adsorption capacity reaches up to 640 mg g−1, which exceeds that of most reported COF-based adsorbents with chemical coordination mechanism in uranium aqueous solution. This ligand engineering strategy can efficiently advance the fundamental understanding of designing the sorbent systems for extraction and remediation technology. [Display omitted] • The COFs were used as bio-inspired folded scaffold structure to regulate the configuration of chelating groups. • The COFs with different configurations were synthesized by introducing isomeric building units. • The optimized configuration provides more UO 2 2+ binding sites without redundant chelating groups introduced. • 2,3-DhaTat-COF achieved high uranium adsorption capacity of 640 mg∙g−1 and short adsorption equilibrium time. • Selectivity for capturing uranium from nuclear wastewater and seawater. [ABSTRACT FROM AUTHOR]