Extraction of rhizoma coptidis alkaloids using aqueous two-phase system of polyethylene glycol (PEG) and ammonium sulfate ((NH4)2SO4). Through the change of the aqueous two-phase system, researched the distribution behavior of four major alkaloids in rhizoma coptidis: berberine, coptisine, palmatine and jatrorrhizin in aqueous two-phase system, and combined with ultraviolet spectrophotometry to detect out the best extraction craft of rhizoma coptidis alkaloids. The best extraction process parameters: pH = 6, T = 20 ℃, PEG1000 mass fraction 20%, ((NH4)2SO4) mass fraction 16%, the highest extraction of berberine, coptisine, palmatine and jatrorrhizin are 99.79%, 98.04%, 99.96%,99.39%, respectively. Aqueous two-phase extraction of rhizoma coptidis alkaloid efficient environmental protection is feasible.