The invention discloses a high-throughput high-retention rate composite nanofiltration membrane preparation method. The preparation method comprises mixing polyetherimide and an organic solvent, carrying out stirring, carrying out standing deaeration to obtain a membrane casting solution, pouring the membrane casting solution on a non-woven fabric, carrying out blade coating and volatilization to obtain a wet membrane, immersing the wet membrane in water, taking out the wet membrane, immersing the wet membrane in an ethene diamine solution for a crosslinking reaction, taking out the membrane, washing the membrane through water, sucking water on the membrane to obtain a crosslinked porous support membrane, fixing the crosslinked porous support membrane between a flat plate and a frame, putting the crosslinked porous support membrane in a constant temperature environment, pouring a water phase aqueous solution into the frame, discharging the solution after the reaction, putting the membrane in a constant temperature environment, removing residual moisture on the membrane surface, pouring a trimesoyl chloride solution into the frame, discharging the solution after a reaction and carrying out drying to obtain the composite nanofiltration membrane. The preparation method has simple processes and can be operated easily. The composite nanofiltration membrane has high throughput, a high retention rate and good membrane stability, can retain micromolecular substances, can be used in a water system and can be used for organic system separation.