The invention discloses a method for separating consensus interferon Alpha (cIFN) isomer by high-speed counter current chromatography. The condition of the high-speed counter current chromatography is as follows: 5-26 percent (w/w) of polyethylene glycol, 7-28 percent (w/w) inorganic or organic acid or salt thereof are mixed with the balance of water, a double water phase system is obtained by the settling, the upper phase is a fixed phase, the lower phase is a mobile phase, and the weight percent uses the total weight of the double water phase system as the reference; the rotating speed of a high-speed counter current chromatography main machine is 600-1200t/min; and the flow rate of the mobile phase is 0.5-1.5ml/min.
