Metal−organic frameworks (MOFs) have attracted considerable attention for selective deep removal of refractory sulfur compounds from fuels. In this work, cobalt-based MOFs (nanocrystals of Co-ZIF-67) were successfully prepared to find a capable adsorbent for removal of dibenzothiophene (DBT) from fuel. This paper revealed the main importance of preparation conditions in adjusting the surface area and pore structure of Co-ZIF-67 crystals for DBT adsorption purposes. Several methods including XRD, SEM, TEM, FTIR, TGA, BET, BJH, and N 2 adsorption−desorption were used for characterization of the prepared adsorbents. Screening the adsorbents demonstrated the proper structure and performance of Co-ZIF-67/M nanocrystals synthesized by methanol at room temperature. A considerable promotion in DBT adsorption ability was further reached through exposing more active centers by surface activation. By employing activated Co-ZIF-67/M-A1 (S BET = 2478.8 m 2 /g), a maximum adsorption capacity of 550 mg/g was attained at T = 65 °C and M adsorbent /V fuel = 0.8 mg/mL, with an excellent reusability of the adsorbent in four repeated uses. The endothermic nature of DBT adsorption was verified by the positive influence of temperature. A good fitting of experimental data with Langmuir−Freundlich isotherm expressed a possible combination of monolayer and multilayer adsorption of DBT. The kinetic and mechanism studies were also conducted, and possible adsorption pathways were suggested.