In numerous reports on selective solid-phase extraction (SPE) of uranium, the extraction of uranium is generally accepted as a direct coordination of the ligands on the solid matrix with the uranyl, in which the critical effect of the hydration shell on the uranyl is neglected. The related mechanism in the extraction process remains unclear. Herein, the detailed calculation of activation energy and the geometry of the identified transition states reveal that the uranium extraction by a newly-synthesized urea-functionalized graphite oxide (Urea-GO) is in essence an exchange process between the ligands on Urea-GO and the coordinated water molecules in the first hydration shell of the uranyl. Moreover, we demonstrate that it is the ketone oxygen in the urea ligand to displace the coordinated water molecule of uranyl due to its stronger bonding ability and lower steric-hindrance, whereas the nitrogen atom in the same ligand is proved to be an electron donor that enables the oxygen atom to have stronger affinity for uranium through electron delocalization effects evaluated on the basis of calculations of the second-order interaction energy between donor and acceptor orbitals. We therefore propose a new ligand-exchange mechanism for the SPE process. This study advances the fundamental understanding of uranium extraction, and provides theoretical and practical guidance on ligand design for selective complexation of uranium(VI) and other metal ions in aqueous solution. Finally, the effect of nitrate ions on the extraction of uranyl was successfully explained based on the experimental and theoretical study.