A density functional theory study was performed to investigate the interactions between 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) and six different model naphthenic acids (NAs). Natural bond orbital, atoms in molecules, noncovalent interactions, HOMO-LUMO overlap integral, and electron density difference were analyzed. The analysis informs on the use of ionic liquids as solvents for the removal of NAs from crude oil. The main extraction mechanism for NAs without long alkyl chain is hydrogen bonding, whereas van der Waals interaction and hydrogen bonding are the dominant extraction mechanisms for NAs with long alkyl chain. F ⋯ H hydrogen bonding is the strongest hydrogen bond, and O ⋯ H is the second strongest for all the interactions. NAs with polycyclic hydrocarbons or multiple carboxylic groups have larger total interaction energies than those with monocyclic hydrocarbons and one carboxylic group. The results indicate that σ(Csingle bondO)-σ*(Csingle bondH), LP(O)-σ*(Csingle bondH), σ*(Csingle bondO)-σ*(Csingle bondH), and σ(Csingle bondH)-σ*(Csingle bondO) interactions can occur between [BMIM][BF4] and model NAs without aromatic ring, whereas π(Csingle bondO)-σ*(Csingle bondH), LP(O)-σ*(Csingle bondH), π*(Csingle bondO)-σ*(Csingle bondH), and σ(Csingle bondH)-π*(Csingle bondO) interactions take place for [BMIM][BF4]-benzoic acid.