Sulfur removal is significant for fuels used as hydrogen source for modern fuel cell applications and to avoid sulfur poisoning of therein used catalysts. Novel membranes for the polymer–zeolite system with well-defined transport channels are proposed for the sulfur removal. Membranes are fabricated using polyimide (PI) as matrix material and Y zeolites as adsorptive functional materials. By detailed analysis of FT-IR, morphology and adsorption performance of membranes, the process-structure-function relationship is obtained. The results show that the functional zeolites particles are incorporated into three-dimensional channels. For 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 sulfur-free hydrogen source for fuel cell applications. The proposed membranes adsorber may be applied as sulfur trap before the reformer for fuel cells on-board or on-site, and it may be applied in a periodically replaceable form. The desulfurization efforts by membrane are likely to play an influential role for the development of sulfur-free hydrogen source and fuel cell area. The well architected three-dimensional membrane channels provided multiple function sites and efficient working way for metal organic frameworks, based which the high performance membrane adsorber with sulfur removal function is expected for modern fuel cell applications. Display omitted •Membranes are proposed for sulfur-free hydrogen source of fuel cell.•Membrane performance is markedly related with three-dimensional transport channels.•Complexation force has significant influence on the adsorption behavior.