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In this study, a particular type of thin film nano-composite membranes was prepared and used in the pervaporation process. The membranes were made of polyphenylsulfone and were coated with a thin layer of polydimethylsiloxane containing different amount of Cu-metal-organic framework (MOF) nano-structures. N-hexane containing dibenzothiophene was used as a model fuel. To characterize MOF and the prepared membranes, Fourier transform infrared, X-Ray diffraction, Brunauer-Emmett-Teller, field-emission scanning electron microscopy, water contact angle measurements, and thermogravimetric analysis were used. The effect of parameters such as sulfur content, process temperature, and Cu-MOF concentration on the membrane performance was evaluated. The results indicated that nano-composite membranes demonstrate a much better performance compared to the untreated membrane. The membrane containing 5 wt% Cu-MOF with a contact angle of 97° had more hydrophilic surface and proved the effect of the additive in improving the surface hydrophilicity. This membrane had the highest rate of flux and rejection (0.4 kg/m 2 h and 70%, respectively), and the lowest enrichment factor (0.3). As the temperature increased, the flux of M 4 membrane (with 5 wt% additive) increased, while the removal efficiency decreased significantly. The optimum temperature for desulfurization in the pervaporation process was obtained (50 °C).