The invention discloses a method for preparing a natural polyelectrolyte nanofiltration membrane and belongs to the technical field of preparation of membrane materials. According to the method disclosed by the invention, a quaternary ammonium cation cellulose ether and a quaternized chitosan blend form an ultra-thin separation layer material, polyvinyl alcohol serves as a casting solution additive, and polysulfone serves as a supporting layer material; two kinds of natural polyelectrolyte serve as a membrane material, and a cross-linking agent is added, so that the two polymers are cross-linked to form a spatial semi-interpenetrating network structure, the polymer networks are mutually tangled, and therefore, the membrane structure stability is enhanced. Meanwhile, the natural polyelectrolyte charged nanofiltration membrane has an antibacterial group capable of inhibiting and killing bacterium components in water, while the membrane structure is provided with many hydrophilic groups,and the hydrophilic property on the membrane surface is excellent. Meanwhile, the raw materials are readily available, the cellulose belongs to renewable resources, the chitosan belongs to natural polysaccharides, any risk of environmental pollution is avoided, and the preparation method is convenient and practical.