Removal of nitrogen-containing compounds from fuel is very important for effective utilization of fuel. In this study, a stable metal-organic framework (MOF, here, MIL-125) and its amino form (MIL-125-NH2) were prepared, and the latter one was further modified to get MIL-125 with various functional groups or MIL-125-NH-C(O)-C(O)-OH. The obtained MIL-125s were applied in the adsorption of both neutral indole (IND) and basic quinoline (QUI) from model fuel in order to estimate the possible applications of the MOFs in adsorptive denitrogenation. MIL-125-NH-C(O)-C(O)-OH, MIL-125-VFG (VFG means various functional groups), showed remarkable performances in the adsorptions. Or, MIL-125-VFG showed the highest adsorption capacity for IND, compared with any adsorbent reported so far. The MOF also showed the second highest uptake of QUI, after the protonated polyaniline(5%)@MIL-101. The remarkable performances of MIL-125-VFG could be interpreted with ample active sites for H-bonding, or the adsorption could be explained via H-bonding (IND: H-donor; QUI: H-acceptor). Moreover, the MOF can be easily recycled by ethanol washing. Therefore, MOFs with ample active sites for H-bonding (or with various functional groups) can be suggested as a promising adsorbent for purification of liquid fuel or adsorptive denitrogenation.