It is critically important to understand the interactions between thiophene/dibenzothiophene/cyclohexane/toluene and 1-methyl-3-octylimidazolium tetrafluoroborate ([C8MIM](+)[BF4](-)) due to desulfurization by ionic liquids. In this work, the structures of thiophene, dibenzothiophene, cyclohexane, toluene, [C8MIM](+)[BF4](-), [C8MIM](+)[BF4](-)-thiophene, [C8MIM](+)[BF4](-)-dibenzothiophene, [C8MIM](+)[BF4](-)-cyclohexane, and [C8MIM](+)[BF4](-)-toluene were optimized systematically at the GGA/PW91/DNP level, and the most stable geometries were performed by NBO and AIM analyses. It was found that [BF4](-) anion tends to locate near C2-H2 and four hydrogen bonds between [C8MIM](+) and [BF4](-) form in [C8MIM](+)[BF4](-). There exist hydrogen bonds and C-H center dot center dot center dot pi interactions between [C8MIM](+)[BF4](-) and thiophene/cyclohexane/toluene, while the hydrogen bonding interactions, pi center dot center dot center dot pi and C-H center dot center dot center dot pi interactions occur between [C8MIM](+)[BF4](-) and dibenzothiophene confirmed by NBO and AIM analyses. The interaction energies between [C8MIM](+)[BF4](-) and thiophene, dibenzothiophene, cyclohexane, toluene are 18.83, 20.93, 6.83, 12.99 kcal/mol, showing the preferential adsorption of dibenzothiophene and thiophene by ionic liquid, in agreement with the experimental results of dibenzothiophene and thiophene extraction by [C8MIM](+)[BF4](-).