The invention discloses a method for modifying flavonoid glycoside compounds with galactosy transferase. The flavonoid glycoside compounds are ubiquitous secondary metabolites in the nature and one of main active ingredients of medicinal plant, and have physiological activities of antibacterium, cancer resistance, antioxidation and the like. However, natural flavonoid glycoside compounds frequently have the defects of poor water solubility, poor drug effect and the like. The method solves the defects of relatively low solubility of the natural flavonoid glycoside compounds and takes the natural flavonoid glycoside compounds as a forerunner to improve the water solubility thereof by a glycosylation reaction, thereby improving the bioavailability thereof. The technical essential of the method is as follows: an enzymatic reaction is applied to the synthesis of polyglycoside of flavonoid compounds. Compared with chemical synthesis methods, the method has higher synthesis efficiency and lower cost. After glycosylation modification, part of drugs can improve drug effect and reduce toxic side effect; therefore, the method provides a new approach for the development of new drugs of the flavonoid compounds.