Selecting an appropriate ionic liquid as extraction solvent for extracting sulfur compounds from fuel, is a promising way to reduce SOx emissions and to prevent environmental pollution. In this regard, the best structural descriptors of different cation and anion, which play an important role on the thiophene distribution between ionic liquid (IL) and hydrocarbon phases in the ternary systems, that is helpful for selecting a proper IL, have been investigated using quantitative structure − property relationship (QSPR) approach. Five different datasets were collected from the literature containing {(Cation/[NTf2] − thiophene − n-heptane), (Cation/[NTf2] − thiophene − n-hexane), (Cation/[FAP] − thiophene − n-heptane), (Cation/[TCM] − thiophene − n-heptane), ([C2MIM]/Anion − thiophene − hydrocarbon), ([C8MIM]/Anion–thiophene − hydrocarbon)} with 664 data points. By investigating the various kinds of molecular descriptors of 1D, 2D and 3D, it was found that the increment of Spanning Tree Number (STN) descriptor as cation structure descriptor, causes a decrease in mole fraction of thiophene in IL-rich phase due to the increase in steric hindrance. STN descriptor reflects the complexity of structure of cation and the information about steric hindrance. Also, it was found that an increase in E1p value as anion structure descriptor leads to the decrement of mole fraction of thiophene in IL-rich phase, in order to increase the interaction between cation and anion in ionic liquid, that reduced the available space of cation to interact with thiophene. The E1p descriptor represents the density of atoms projected along the length or unfilled space of the anion, thus it is informative of the accessibility of them by thiophene.