The invention discloses a preparation method of an anionic water-based polyurethane emulsion. A RAFT (reversible addition-fragmentation chain transfer) emulsion polymerization system is selected in the preparation method; and the hydrophilic group is introduced through the introduction of dimethylolpropionic acid and dihydroxymethylbutyric acid low-molecular hydrophilic monomers, or introduced by regulating a polyacrylic acid-b-polystyrene block copolymer high-molecular RAFT reagent and a polyacrylic acid-b-polymethyl methacrylate block copolymer high-molecular RAFT reagent amphiphilic monomer with a RAFT reagent by a self-emulsifying process. The invention discloses a synthesis method of the water-based polyurethane emulsion by RAFT emulsion polymerization. The active free-radical polymerization process is utilized to synthesize the water-based polyurethane with controllable molecular weight and lower molecular weight distribution. The method has the advantages of simple technique and mild conditions, and is convenient for industrial production.