The invention discloses a method for removing organic residue in heparin sodium through vacuum drying. The method comprises the following steps of: adding a wet solid ethanol precipitate obtained after aseptic filtration in the process of the refinement of a crude product of the heparin sodium into ethanol at the concentration of between 90 and 99 percent for dehydration treatment; repeatedly performing dehydration treatment on the precipitate treated in the previous step by adopting ethanol at the concentration of between 80 and 90 percent for 1 to 4 times; and performing vacuum drying on the precipitate for over 20 hours at the temperature of between 30 and 75 DEG C under the relative vacuum degree of less than or equal to -0.09MPa to obtain a refined product of the heparin sodium, wherein the temperature is not more than 50 DEG C within early 5 to 10 hours of vacuum drying. The refined product of the heparin sodium prepared by the method ensures that the content of the ethanol is less than 0.5 percent and can further reach below 0.1 percent on the basis of ensuring the quality of the heparin sodium. The method also has the advantages that: the energy consumption is low, the cost is low, small area is occupied in clean area, the product batch is easy to enlarge and the performance is steady.