The water purification efficiency and flux attenuation of nanofiltration working in different permeate ratios were contrasted and performance of NF under 90% permeate ratio was investigated. MBR was employed to combine NF for micro pollutant water resource treatment. The ammonia-N and TOC removal capability of the hybrid system was studied. Furthermore, membrane fouling processes of both UF membrane in MBR and NF membrane were investigated. Since the permeate ratio of NF enhanced from 15% to 90%, TOC removal rate and the desalination rate declined by 4% and 3.5%, respectively, when NF remained effective rejection of pollutants. However, NF flux decline by 17%. The result indicated that reduction of TOC concentration in NF influent could slower the fouling process of NF. The MBR-NF system showed high pollutants removal efficiency even that flux ratio of NF was as high as 90%. The concentration of ammonia-N and TOC reduced from 1.5mg/L, 3.5mg/L to 0.4mg/L and 0.2mg/L, respectively. Due to the high removal of particulate and organic matters in MBR, NF fouling process was obviously relieved that 24.7% of flux decline was observed during 60 days operation.