There is limited research on the relationship between membrane fouling and microbial metabolites in the nitrogen removal process coupled with membrane bioreactors (MBRs). In this study, we compared anoxic-oxic (AO) and partial nitritation-anammox (PNA), which were selected as representative heterotrophic and autotrophic biological nitrogen removal-coupled MBR processes for their fouling behavior. At the same nitrogen loading rate of 100 mg/L and mixed liquor suspended solids (MLSS) concentration of 4000 mg/L, PNA-MBR exhibited more severe membrane fouling compared to AO-MBR, as evidenced by monitoring changes in transmembrane pressure (TMP). In the autotrophic nitrogen removal process, without added organic carbon, the supernatant of PNA-MBR had higher concentrations of protein, polysaccharides, and low-molecular-weight humic substances, leading to a rapid flux decline. Extracellular polymeric substances (EPS) extracted from suspended sludge and cake sludge in PNA-MBR also contributed to more severe membrane fouling than in AO-MBR. The EPS subfractions of PNA-MBR exhibited looser secondary structures in protein and stronger surface hydrophobicity, particularly in the cake sludge, which contained higher contents of humic substances with lower molecular weights. The higher abundances of Brocadia and in PNA-MBR could lead to the production of more hydrophobic organics and humic substances. Hydrophobic metabolism products as well as anammox bacteria were deposited on the hydrophobic membrane surface and formed serious fouling. Therefore, hydrophilic membrane modification is more urgently needed to mitigate membrane fouling when running PNA-MBR than AO-MBR.