The invention discloses a method for preparing amygdalin, comprising the following steps: S1, preparation of an extract: fetching a bitter apricot kernel medicinal material as a raw material, crushing and sieving, carrying out enzyme deactivation, degreasing, filtering and fetching filter residue, dissolving with alcohol, carrying out ultrasonic extraction, filtering, and concentrating a filtrate to obtain an extract mainly containing amygdalin; S2, normal phase column chromatographic separation: using ethyl acetate-methanol as an elution solvent and using silica gel as a filling material and carrying out normal phase column chromatographic separation on the extract of amygdalin, collecting the elution solvent containing amygdalin, and carrying out reduced pressure distillation to obtain an amygdalin crude product; and S3, high-speed counter-current chromatographic purification: using ethyl acetate-n butanol-water as a solvent system, and carrying out high-speed counter-current chromatographic purification on amygdalin. By the above preparation method, purity of the prepared amygdalin is high, and one-time preparation amount is large. There is no influence on activity of the sample, and there is no additional pollution. The product can be applied to medicines, cosmetic, health products and the like.