A membrane adsorber with hierarchically porous HKUST-1 (HP-HKUST-1) immobilized in membrane pores has been fabricated by flowing synthesis. The XRD characteristics indicated that the structure integrity of the HP-HKUST-1 immobilized in the membrane pores can be kept after template agent removed. Other characteristics presented by XPS, FTIR, SEM, TEM and BET proved the effective immobilization of HP-HKUST-1 in membrane pores. Compared with hydrothermal HKUST-1 powder, the adsorption capacity for Congo red and Methylene blue adsorption can be increased several times by hydrothermal HP-HKUST-1 powder, owing to the mesopores with rich active sites for adsorption. When the solution was flowed through the membrane adsorber, the adsorption rate for these adsorbates increased significantly, owing to the enhanced mass transfer in the confined space of the membrane pores with micro or nano scale. After going through seven adsorption-desorption experiments, the membrane adsorber with HP-HKUST-1 immobilized in membrane pores shows a remarkable repeatability.