The influence of the functional groups in MM-101(Cr)-X metal-organic frameworks (MOFs) with X = H, NH2, and NO2 on the adsorption properties of N/S-heteroaromatic compounds from model fuels was investigated. Benzothiophene (BT), dibenzothiophene (DBT), quinoline, and indole were selected as representative organosulfur and organonitrogen contaminants in liquid fuels. Their adsorption on four MIL-101 materials from model fuels was evaluated in a batch adsorption system. Introducing amino or nitro group into MIL-101(Cr) leads to decreased adsorption capacities of BT and DBT from isooctane, especially the bulkier nitro group. The adsorption capacities of indole and quinoline from isooctane also decrease when introducing nitro group. However, the adsorption capacities of quinoline and indole on amino-MIL-101(Cr) increase by about 25% and 10% even through the porosity is 30% lower than that of the parent. The improved adsorption capacities of amino-MIL-101(Cr) for quinoline and indole are attributed to hydrogen bonding between the -NH2 group and organonitrogen compounds. MIL-101(Cr)-NH2 can retain most of its capacity for quinoline in the presence of substantial amounts of aromatics, making it a potential adsorbent for the deep denitrogenation of fuels.