The invention relates to a novel method for extracting anthocyanin in bilberry by double water phases, and belongs to the technical field of biological engineering. The method is characterized by comprising the following steps: adding inorganic salt solution and hydrophilic low-molecular organic substance into bilberry fruit residue, stirring the mixture evenly, keeping the mixture standing, layering the mixture, extracting the anthocyanin to an upper phase, and distributing the residue at the lower phase or between the two phases so as to achieve the aim of extracting the anthocyanin from the bilberry fruit residue. The inorganic salt is one or a combination of sodium chloride, ammonium sulphate, sodium sulfate, sodium carbonate, potassium carbonate, potassium phosphate, monopotassium phosphate and dipotassium hydrogen phosphate, preferably ammonium sulphate; and the hydrophilic low-molecular organic substance is one or a combination of methanol, ethanol, normal propyl alcohol, isopropyl alcohol, normal butanol, isobutyl alcohol, glycol and acetone, preferably ethanol. The method has the advantages that a novel method for extracting the anthocyanin is developed, the method is easy to industrialize, the utilization ratio of the bilberry is improved, and the production cost of the anthocyanin is lowered.