The invention discloses a method for separating cerebroside from sea cucumber by a high-speed countercurrent chromatography, which is characterized by comprising the following steps of: adding mixed solution of chloroform and methanol into sea cucumber dry powder, soaking at room temperature, and concentrating filter liquor to obtain a cerebroside crude extract; mixing petroleum ether, methanol and water, and respectively performing ultrasonic degasification on the formed stationary phase and mobile phase; dissolving the crude extract by using the mixed solvent, and filtering to obtain samplesolution; and pumping the stationary phase into a chromatographic column of the high-speed countercurrent chromatography, adjusting the rotating speed of a main machine and the flow rate of the mobile phase, pumping in the mobile phase, after two phase equilibria, pumping the sample solution into the chromatographic column through an introduction valve, continuously pumping in the mobile phase, collecting by steps, detecting by using a thin layer chromatography, merging the target object, concentrating, and freeze-drying to obtain the cerebroside. The preparation process has the advantages ofsimpleness, simple and convenient operation, high purification efficiency, short separation time, high stability, and suitability for separation of the cerebroside from various sea cucumber samples and industrial production.