Polyimide (PI) is a type of important membrane material. A soluble polymer was synthesized from 4,4´-(hexafluoroisopropylidene) diphthalic anhydride (6FDA) and 2,2-bis[4-(4-aminophenoxy) phenyl] hexafluoropropane (BDAF) by the two-step polymerization method. The polymer was proved to be polyimide 6FDA-BDAF by the Fourier transform infrared (FT-IR), the 1H-NMR and 19F-NMR spectra. An asymmetric membrane was prepared with the synthesized polyimide 6FDA-BDAF, it was porous in the 50 μm height bulk and dense in a 3–5 μm height surface. The membrane was used to separate n-heptane/ thiophene mixtures by pervaporation with sulfur (S) contents from 50 to 900 μg g–1. The total flux was enlarged from 7.96 to 37.61 kg m–2 h–1 with temperature increasing from 50 to 90°C. The membrane’s enrichments factor for thiophene were about 3.13 and dependent on the experimental conditions. The experimental results demonstrated that polyimide 6FDA-BDAF would be a potential membrane material for desulfurization and controlled release of the S-containing fertilizer.