Sulphur removal is significant for fuels used as hydrogen sources for modern fuel cell applications. A high performance membrane adsorber with metal organic frameworks (MOFs) has been fabricated. The architecture of the three-dimensional membrane channels provided multiple functional sites and an efficient method of incorporating [Cu₃(BTC)₂] particles into a polyimide (PI) matrix. The properties of the MOF-based membrane adsorber, including the adsorption contribution, regeneration behavior and effect of fuel species, have been investigated. In all cases, the inlet fuel can be desulfurized to below 0.1 mg L⁻¹, which means that the outlet fuel can be used as a sulphur-free hydrogen source for fuel cell applications. The related discussions can propose some general suggestions for the separation of organic–organic mixtures involved in current energy and environmental problems. The desulfurization capabilities of the membrane adsorber are likely to play an influential role in the reduction of motor vehicle pollution and the development of fuel cells.