Membrane hydrophilic modification has been applied as an effective antifouling strategy for aerobic and anaerobic heterotrophic membrane bioreactors (MBRs), while its antifouling performance remains unclear for anaerobic ammonium oxidation (anammox) MBR. Herein, hydrophilic membranes (M-h) modified from pristine nylon fabric meshes (M-p, pore size of 20 mu m), were applied in long-term operation of an anammox MBR. Although the average flux of M-h was 90.7% higher than that of M-p < 0.05) filtered with model foulant (bovine serum albumin) in a dead-end filtration test, the average filtration cycle of M-h in the anammox MBR was 37.9% shorter than that of M-p filtered with synthesized wastewater, in spite of the comparable total nitrogen removal efficiency (over 80%) achieved. A thin and compact gel layer was formed on M-h by adsorption of hydrophilic polysaccharide and further gelation of protein and colloidal biomass. The bound water wrapped in the gel layer on M-h brought about 32.8% higher filtration resistance, and caused 81.3% higher contribution rate of the flux decline caused by concentration polarization, compared with M-p. Moreover, more microbial metabolites, especially protein (23.9% vs. 17.7%), was rejected by M-h than M-p, providing organic matters for the proliferation of heterotrophic bacteria, and leading to the decreased relative abundance of anammox bacteria (from 63.2% to 35.2%). We proposed the formation process of the gel layer and revealed the membrane fouling mechanism on M-h in the anammox MBR, providing significant theoretical foundation for the membrane fouling control of anammox MBR systems.