Abstract: To separate the total flavonoids from Houttuyniae cordata Thunb. by aueous two- phase systems composed of polyethylene glycol( PEG) and phosphate salts,an orthogonal experimental design method was applied to evaluate the influence of the average molecular mass of PEG,mass ratio of the two phases,temperature and p H value on total flavonoids extraction.The extraction rate was achieved 98.96% under the optimal conditions:mPEG400∶ m( NH4) 2SO4= 2.0 ∶ 2.0,temperature was 50 ℃,p H was 3.0. The result indicated that the aqueous two- phase extraction was simple,high quality and environment friendly,and also could apply some useful information for the efficient use of the total flavonoids in Houttuyniae cordata Thunb..