The invention discloses an enzymatic synthesis method for heparin. The enzymatic synthesis method comprises the following steps: raw material cleaning, raw material processing, primary enzymolysis, secondary enzymolysis, extraction, adsorption, elution, precipitation as well as drying and acidification. The synthesis and extraction efficiency of heparin sodium is increased effectively by regulating the preparation method reasonably, then the heparin yield is increased, the loss of activity of heparin sodium is reduced, the quality of the synthesized heparin is guaranteed, and the enzymatic synthesis method is mild in production condition, environment-friendly, low in energy consumption and high in efficiency and reduces the synthesis cost of the heparin.