The invention discloses a method for extracting total flavonoids in grape seeds in a double-aqueous phase system, belonging to the field of separation and extraction methods of natural product active ingredients. The method comprises the following steps of: firstly preparing grape seed rough extract from grape seeds with ethanol; then adding absolute ethyl alcohol, ammonia sulfate, inorganic salt and water in the grape seed rough extract to form the double-aqueous phase system, mixing uniformly, standing for 5-30 minutes at room temperature for delamination to obtain an upper phase and a lower phase, concentrating the upper phase through pressure reduction and drying so as to obtain total flavonoids of grape seed. In the double-aqueous phase system, the mass percents of grape seed rough extract, absolute ethyl alcohol, ammonia sulfate and inorganic salt are respectively 5% to 30%, 10% to 30%, 16% to 30%, and 0 to 5%, the balance is supplemented to be 100% with water, and the pH of the double-aqueous phase system is 3.0 to 11.0. Flavonoids are extracted by utilizing double aqueous phases in the method; the method is simple, the operation is convenient, the production cost is low and the treating capacity is large, small test data can be directly amplified, and the yield of flavonoids in the grape seeds reaches up to 98.2%; and the method can be operated continuously, and is suitable for industrialized production of flavonoids in the grape seeds.