Membrane technology is attractive for natural gas separation (removing CO₂, H₂O, and hydrocarbons from CH₄) because of membranes’ low energy consumption and small environmental footprint. Compared to polymeric membranes, microporous inorganic membranes such as silicoaluminophosphate-34 (SAPO-34) membrane can retain their separation performance under conditions close to industrial requirements. However, moisture and hydrocarbons in natural gas can be strongly adsorbed in the pores of those membranes, thereby reducing the membrane separation performance. Herein, we report the fabrication of a polycrystalline MIL-160 membrane on an Al₂O₃ substrate by in situ hydrothermal synthesis. The MIL-160 membrane with a thickness of ca. 3 μm shows a remarkable molecular sieving effect in gas separation. Besides, the pore size and environment of the MIL-160 membrane can be precisely controlled using reticular chemistry by regulating the size and functionality of the ligand. Interestingly, the more polar fluorine-functionalized multivariate MIL-160/CAU-10-F membrane exhibits a 10.7% increase in selectivity for CO₂/CH₄ separation and a 31.2% increase in CO₂ permeance compared to those of the MIL-160 membrane. In addition, hydrophobic MIL-160 membranes and MIL-160/CAU-10-F membranes are more resistant to water vapor and hydrocarbons than the hydrophilic SAPO-34 membranes.