Separation of sulfides from fluid catalytic cracking (FCC) naphtha is of great significance for environmental protection. In this work, the organic solvents N-methyl-2-pyrrolidone (NMP), sulfolane (SUL), and their mixtures were selected to extract sulfides (3-methylthiophene) from model FCC naphtha (n-heptane). Correspondingly, the liquid-liquid phase equilibrium (LLE) data of the systems n-heptane +3-methylthiophene + SUL/NMP/(NMP + SUL) were experimentally obtained at 298.15 K and 101.3 kPa. The distribution coefficient and separation factor were calculated to assess the extraction performance of the solvents. The results showed that mixed solvent (NMP + SUL) could be used as a potential solvent to extract 3-methylthiophene due to its suitable selectivity and solubility. Meanwhile, the density functional theory (DFT) method was applied to explore the extraction mechanism of 3-methylthiophene from n-heptane by NMP or SUL. Electrostatic potential (ESP) analysis, interaction energies, and reduced density gradient (RDG) analysis showed that the main interactions between NMP/SUL and 3-methylthiophene were van der Waals and weak hydrogen bond forces. In addition, the LLE data were correlated by the NRTL and UNIQUAC thermodynamic models with the RMSD values were all <0.30%. Also, the binary interaction parameters were regressed which could be applied for the optimization and design of the separation process.