Ionic liquids (ILs) have shown an excellent performance for removing the sulfur compounds of fuel. In this work, molecular dynamic simulations were performed to screen suitable IL instead of the traditional method which is inefficient. DBT and DBTO2 were used as model compounds to study the mechanism of desulphurization. An all-atom force field was proposed for dibenzothiophene (DBT) and dibenzothiophene 5,5-dioxide (DBTO2). The calculated results are in good agreement with the experimental value. We investigated the interaction between the model compounds and a series of ILs composed of 1-alkyl-3-methylimidazolium cations ([C-nmim](+), n = 4, 6, 8, 10) and BF4-, PF6- anions. We found that the interaction between hydrogen atoms in imidazolium ring and oxygen atoms in DBTO2 is stronger than that of sulfur atoms in DBT, and it means that DBTO2 is extracted by ILs more easily than DBT. In this work, we also compared and discussed the desulphurization mechanism as a function of different ILs, sulfur contents, temperatures, and inclusion of water or not. The above results may help us design extractant and improve the operating conditions. (C) 2010 American Institute of Chemical Engineers AIChE J, 56: 2983-2996, 2010