The invention discloses a preparation method of a high-throughput and multilayer sandwich type composite nano-filtration membrane. The preparation method includes: performing surface modification on an ultrafiltration basement membrane and (zero-dimensional or one-dimensional and two-dimensional) nano materials to allow the ultrafiltration basement membrane and the nano materials to be electronegative, and using cationic polyelectrolyte as the bridge to alternatively assemble the one-dimensional or zero-dimensional nano materials and two-dimensional sheet layers onto the ultrafiltration basement membrane to obtain the high-throughput composite nano-filtration membrane with a functional layer being two-dimensional nano materials sandwiched with one-dimensional or zero-dimensional nano materials. The preparation method has the advantages that the difficulty that the interlayer spacing of a two-dimensional nano layered membrane is small and the two-dimensional nano layered membrane is easy to deform during high-pressure filtration is solved effectively by the prepared functional layer, membrane throughput can be increased evidently, and the long-term stability of the membrane structure can be kept at the same time; the preparation method is simple in preparation process, and the prepared nano-filtration membrane is high in throughput and promising in application prospect in fields such as dye removing.