The invention discloses a method for preparation of 6'-malonyl formyl ginsenoside F1, including: step 1: smashing ginseng flower bud, using 95% ethyl alcohol to extract by hot reflux, obtaining totalextractive in paste by concentration; step 2: dissolving the total extractive with 25% ethyl alcohol and regulating the concentration to be 0.2 g crude drug / ml, filtering, loading quantity of sample is 0.8 BV, column bed diameter height ratio of LX-68 large hole absorption resin column is 1:9, using 40% ethyl alcohol of 3 BV to remove impurities first, then using 75% ethyl alcohol of 9 BV to elute, collecting eluent of 75% ethyl alcohol eluent of 8-9 BV, decompressing and concentrating until no alcohol exists, then performing freeze-drying to obtain crude lyophilized powder; step 3: performinghigh-speed countercurrent separation: the solvent system is n-butyl alcohol / ethyl acetate / methanol / water / chloroform with a volume ratio of 1:18:1:18:0.5, collecting elution flow components corresponding to 6'-malonyl formyl ginsenoside F1, obtaining 6'-malonyl formyl ginsenoside F1 after concentration.