Biofouling remains one of the most challenging issues of membrane application in water industry. One of the practical strategies to control fouling is anti-biofouling membrane. High concentration and high stable biogenic nanoparticle silver with the averaged diameter of only 6 nm (Bio-Ag0-6) was firstly extracted from the supernatant of Lactobacillus fermentum. The biogenic nanocomposite polyethersulfone (Bio-Ag0-6/PES) membranes were prepared by adding different amounts of biogenic nanoparticle silver into the dope solution. The nanocomposite membranes were systematically tested for physical properties with pure water permeability, MWCO (molecular weight cut-off), contact angle, scanning electron microscopy (SEM) and atomic force microscopy (AFM). The results demonstrated that the Bio-Ag0-6 nanoparticles well dispersed into PES matrix without aggregation. Bio-Ag0-6 slightly increased the hydrophilicity of the PES membranes, improved the water permeability and did not sacrifice the selectivity of BSA. The protein adsorption on the membrane surface decreased significantly due to the increased hydrophilicity and the improved smoothness of membrane surfaces. The evaluation of silver release from the composite membranes indicated the good stability of immobilized Bio-Ag0-6 in the membranes. The results of disk diffusion test revealed the excellent antibacterial activity of the nanocomposite membranes. In addition, the sludge immersion and the bacterial suspension filtration experiments showed that the Bio-Ag0-6/PES composite membranes not only prevent the bacteria attachment on the membrane surface but also inhibit the reproduction and development of biofims. The Bio-Ag0-6/PES composite membranes were considered to be an effective strategy to decrease the biofouling in the membrane process.