Membrane fouling in membrane bioreactors (MBR) normally depends on the microbial cell density and microbial population structure. A nitrifying-enriched activated sludge (NAS) was obtained in this study through particular ammonium feeding of conventional activated sludge (CAS). Next, the dominance of autotrophic nitrifler population in NAS system was checked and compared with CAS system by its high nitrification efficiency (100% vs. 43%) and low COD removal (9% vs. 65%). Furthermore, the maximum amount of N-NO3-produced from similar concentrations of ammonium in CAS and NAS systems were 6.6 mg/L and 37.5 mg/L, respectively. A filterability test also was done in the cross-flow and simple dead-end filtration systems proportionally employing different amount of NAS and CAS with a constant MLSS concentration of 2000 mg/L. NAS was twice as filterable compared to CAS. Soluble microbial products (SMP) and extracellular polymeric substance (EPS) in CAS were significantly higher than NAS system (2 and 6 mg/L for NAS vs.100 and 36 mg/L for CAS). By increasing the proportion of nitrifying bacteria, the permeation was enhanced remarkably about 2.5 folds and the operation time of MBR was approximately doubled (6-11.5 h). The results indicated that an appropriate C/N ratio can control the microbial population and help the nitrifier significantly mitigate fouling in MBR.