In this study, flake-like reduced graphene oxide (rGO) was integrated with filamentous carbon nanotube (CNT) in different ways to prepare CNT-rGO composite membranes with three distinctive types of nanostructures. These membranes were further assessed at bench scale to determine the relationship between nanocomposite structure and membrane performance, including clean water permeability, removal efficiencies for pharmaceuticals and personal care products (PPCP), and resistance to organic fouling. Among the three types of prepared membranes, the membrane with CNT evenly distributed in the rGO layer outperformed other membranes in terms of PPCP removal efficiencies (76-100%), clean water permeability (4454 L m(-2) h(-1) bar(-1)), and antifouling property. Further membrane characterization using scanning electron microscopy and other analytical techniques revealed that the outstanding performance of this membrane resulted from the open CNT-rGO nanostructure that was beneficial for water permeation, PPCP adsorption, and membrane fouling reduction. Overall, these results demonstrated that, under the condition of similar compositions and surface properties, the nanostructures of CNT-rGO membranes significantly influenced membrane performance. Therefore, it is feasible to manipulate the nanostructures of CNT-rGO composite membranes to achieve high clean membrane permeability, outstanding antifouling property, and efficient contaminant removal.