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A computational study was firstly performed in this work to examine the applicability of an acid-functionalized metal-organic framework (MOF), UiO-66(Zr)-(COOH)2, in membrane-based H2S/CH4separation. The results show that this MOF could be potentially interesting when being used as the pure membrane material for the separation of the mixture with low H2S concentration. Further, the performance of 10 different mixed matrix membranes (MMMs) on the basis of the MOF was predicted by combing the molecular simulation data and the Maxwell permeation model. The results indicate that using this MOF as filler particles in MMMs can significantly enhance the permeation performance of pure polymers. The findings obtained in this work may be helpful in facilitating the application of this promising MOF for practical desulfurization process of fuel gas.