This study investigated the impact of membrane pore morphology on repeated fouling and physical cleaning behavior during> 1000 h operation of a membrane bioreactor process. Four microfiltration membranes with different backbone polymers (PVDF and PTFE) and varied hydrophobicity, operated in parallel, were compared. The PVDF membranes presented a porous particulate-packing morphology, while the PTFE/ PVDF blend membranes (PTFE accounting for > 80% of monomer proportion) resembled a nonwoven network of thin fibrous material. These membranes had similar short-term apparent fouling rates in a single fouling-and-cleaning cycle, but different long-term fouling development due to their physical cleaning efficiencies differing in the order: hydrophobic PVDF < < hydrophobic blend < hydrophilic (PVDF and blend) membranes, as revealed by statistical analyses. The physically irreversible fouling was likely attributed to hydrophobic adsorption onto the membranes, with the adsorbed polysaccharides and proteins detected using confocal laser scanning microscopy. The irreversibility of fouling on the blend membranes was much less sensitive to membrane hydrophobicity than that on the PVDF membranes, probably because the blend membranes had smaller adsorption propensity. For further evidence, the adsorption properties of the membranes were explored via batch tests of dynamic adsorption using model compounds, with the adsorption rate and equilibrium constants quantified using the Thomas model. The thin thread-like pore walls (which characterized the morphology of the blend membranes) may provide limited contact area for foulant adsorption, and/ or weaken the interfacial membrane-foulant interaction via shape effect. Therefore, it is suggested that membranes with thin fibrous network-like pore morphology may perform more robustly and be less troubled by adsorptive irreversible fouling for long-term operation of MBR.