The invention provides a method for preparing an intermediate of acetonyl geranyl pyrophosphate. Farnesol is used as a raw material, hydroxyl group is protected, and then an epoxy intermediate is prepared, which is cut by epoxy to form an aldehyde, and then mixed with methyl Grignard reagent. Reaction, re-oxidation of hydroxyl group, deprotection to obtain (5E, 9E)-11-hydroxyl-5,9-dimethylundec-5,9-dien-2-ketone 7, then hydroxy halogenation, then with pyrophosphoric acid A salt reaction is performed to finally obtain acetonyl geranyl pyrophosphate. The method is cheap to synthesize, has mild reaction conditions, and has less isomer impurities, and is suitable for scale-up production.