Objective: Extracting ephedrine and berberine from the water extract of Ephedra Herba and Rhizoma Coptidis. Methods: Modified PVA was used as separating membrane and separated alkaloids. Results: A colorless ephedrine aqueous solution was obtained when extraction time was less than 8 hours; while a three constitution solution was obtained when time of extraction is over 8 hours. So is Rhizoma Coptidis. The membrane is hardly fouled. Conclusion: Purity of alkaloids from Herba Ephedra and Rhizoma Coptidis by membrane separation is Superior to that by alcoholic sediment but amount of alkaloids is reverse.