This paper serves as a molecular dynamics (MD) study on the desulfurization of diesel oil model using magnetic ionic liquids (MILs). In this regard, three different MILs, namely, [emim][FeCl4], [bmim][FeCl4] and [hmim][FeCl4] have been used to remove the dibenzothiophene (DBT) from n-dodecane as diesel oil model. The effects of alkyl chain length of cation in MIL, temperature, initial sulfur content and mass ratio of MIL to diesel oil on two vital parameters of desulfurization process i.e. percentage of S-removal and Nernst partition coefficient (KN) were investigated. These two parameters were calculated based on the method proposed by Feng and Mi (Ind. Eng. Chem. Res. 2014, 53, 20234-20240), in which they used the radial distribution function (RDF) plots obtained by Conductor-like Screening Model for Real Solvents (COSMO-RS) to evaluate the desulfurization of fuel oil, quantitatively. Our results showed that the [bmim][FeCl4] has the highest DBT-philisity and its S-removal efficiency increases with increasing temperature and the concentration of the MIL. Furthermore, from the investigation of the initial sulfur content in diesel oil model it is concluded that the MIL can be a good extractor for oil refinery applications with a wide range of sulfur content in diesel oil. The results of RDF and combined distribution function (CDF) plots and also Voronoi tessellation analysis showed that the DBT molecules are adsorbed mainly by the MIL molecules compared with the n-dodecane which leads to DBT-removal. Also, it is found that the DBT molecules interact with the cation of MIL more than its anion. The results of domain analysis showed that the n-dodecane subset is stiffer than the MIL and DBT subsets. Altogether, the Fe-containing MILs can be a good sulfur extractor with high S-removal efficiency, lower toxicity than common volatile organic solvents, and low cost compared to the other common methods such as hydrodesulfurization (HDS), for future oil refinery applications.