Although metal–organic frameworks offer a new platform for developing versatile sorption materials, yet coordinating the functionality, structure and component of these materials remains a great challenge. It depends on a comprehensive knowledge of a “real sorption mechanism”. Herein, a ternary mechanism for U(VI) uptake in metal–organic frameworks was reported. Analogous MIL-100s (Al, Fe, Cr) were prepared and studied for their ability to sequestrate U(VI) from aqueous solutions. As a result, MIL-100(Al) performed the best among the tested materials, and MIL-100(Cr) performed the worst. The nuclear magnetic resonance technique combined with energy-dispersive X-ray spectroscopy and zeta potential measurement reveal that U(VI) uptake in the three metal–organic frameworks involves different mechanisms. Specifically, hydrated uranyl ions form outer-sphere complexes in the surface of MIL-100s (Al, Fe) by exchanging with hydrogen ions of terminal hydroxyl groups (Al-OH2, Fe-OH2), and/or, hydrated uranyl ions are bound directly to Al(III) center in MIL-100(Al) through a strong inner-sphere coordination. For MIL-100(Cr), however, the U(VI) uptake is attributed to electrostatic attraction. Besides, the sorption mechanism is also pH and ionic strength dependent. The present study suggests that changing metal center of metal–organic frameworks and sorption conditions alters sorption mechanism, which helps to construct effective metal–organic frameworks-based sorbents for water purification.