In this paper, copper benzene-1,3,5-tricarboxylate (CuBTC) was incorporated into polyethylenglyol (PEG) to prepare a mixed matrix membrane (MMM) for pervaporation desulfurization. The characterization results showed that the prepared CuBTC particles had an ideal octahedral shape and micropores. The Cu2+ in CuBTC interacts with thiophene via π-complexation, thus enhancing the separation performance of the hybrid membranes. The effect of CuBTC content and the operating condition on the pervaporation performance of the MMMs was investigated. An optimal pervaporation separation performance was acquired with a permeation flux of 2.21 kg/(m2·h) and an enrichment factor of 8.79, which were increased by 100% and 39% compared with the pristine PEG membrane. Moreover, the CuBTC-filled PEG membrane showed a good stability in the long-term desulfurization under a high operating temperature of 75 °C for five days.