Highly selective adsorption capacity is critical for meeting the challenge of deep removal of thiophene-based sulfurs from oil. How to regulate the active metal sites in metal organic frameworks (MOFs) to enhance the adsorption performance have been long sought after. Herein, the open metal sites with higher valence state are successfully constructed in bimetallic organic frameworks of MIL-47(xV/Cr)-Brs. The density function theory calculations and the spectra analysis reveal that not only the enhanced Metal-S and π-π interactions, but also the H-Bond between µ2-OH and S of thiophene synergistically improve the desulfurization performance, resulting in excellent capacity of 256 mgS g−1 and high selectivity of thiophene/aromatics. Even in a harsh operation condition of water presence in oil, MIL-47(2V/Cr)-Br maintains its superior capacity, exceeding all the reported works so far as we know. More significantly, the continue flow desulfurization from the commercial oil further demonstrate the advantages of bimetallic MOF in the practical adsorptive desulfurization, which may pave a way for understanding and designing novel hetero-metallic sorbents for adsorption and separation.