Hydrodesulphurization (HDS) is a standard process for removing sulphur compounds in fuel oils in industry. HDS is effective to remove simple aliphatic sulphur compounds while less effective to remove thiophenes, dibenzothiophenes, and their derivatives because of sterically hindered adsorption on catalyst surface. Application of ionic liquids (ILs, a new class of compounds) substituting for traditional volatile organic solvents in extractive desulphurization (EDS) or oxidative desulphurization (ODS), have been being studied intensively in the latest decades, and many very promising results have been obtained, showing a good prospect as complement method to HDS. In this chapter, these fresh research results of EDS and ODS using ILs are summarized along with comprehensive discussions on diversified desulphurization factors along with some potential problems. It can be inferred that ILs are a class of potential ideal solvents to realize clean fuel oil in future although some problems come too. © 2016 by IGI Global. All rights reserved.