The invention relates to a method for separating and extracting cepharanthine, which comprises the following steps of: taking a dry stephania tuberous root, crushing, adding 2 to 3L of water and 0.5 to 5ml of mixed bio-enzyme liquid into each kilogram of crushed material, soaking for 1 hour, adding 9 to 11L of 1 to 2 mass percent aqueous solution of HCL, heating to 90DEG C, and soaking for 3 hours; and separating out a liquid medicine, adding 9 to 11L of 1 to 2 percent aqueous solution of HCL into dregs, decocting for 3 hours, filtering, mixing filtrate, adsorbing by adopting a cation exchange column or cation cellulose column, enriching the cepharanthine, eluting by using solution that sodium hydroxide is added into 60 to 90 percent aqueous solution of ethanol until the saturation state as eluent, collecting eluent of a cepharanthine section, regulating the pH value to be 7, concentrating for recovering ethanol, filtering, dissolving a precipitate by using absolute ethanol, eluting and purifying by using an anion column, collecting eluent of a cepharanthine section, concentrating, crystallizing, and drying to obtain the cepharanthine. The method has the advantages of simple operation, light pollution, low cost, high yield, high purity of cepharanthine, and suitability for industrial production.