In this work, the adsorption of thiophene on the Mg4O4 cluster was examined at the LC-ωPBE/6-311G(d,p) level of theory. The influence of replacing hydrogen atoms of thiophene with fluorine atoms was considered. The comparison of relative stabilities of possible isomers indicated most stable isomers were 3-FT … Mg4O4, 3,4-DFT … Mg4O4, 2,3,4-TFT … Mg4O4 structures in the mono, di and tri-fluorinated thiophenes, respectively. Corrected adsorption energy and thermodynamic parameter values of these systems were evaluated and the substituent effect on the adsorption was explored. 2-FT … Mg4O4, 3,4-DFT … Mg4O4, 2,3,4-TFT … Mg4O4 structures indicated the most significant adsorptions in the mono, di and tri-fluorinated thiophenes, respectively. Electrophilicity-based charge transfer (ECT) was employed to illustrate charge transfer between aromatic systems and the Mg4O4 cluster. Quantum theory of atoms in molecule (QTAIM) and interaction region indicator (IRI) were used to deeply investigate two fragments.