The invention provides a geranyl acetone pyrophosphate intermediate preparation method, which comprises: carrying out hydroxyl protection on farnesol as a raw material, preparing an epoxy intermediate, carrying out epoxy cutting to obtain an aldehyde, carrying out a reaction with a methyl Grignard reagent, oxidizing the hydroxyl, deprotecting to obtain (5E,9E)-11-hydroxy-5,9-dimethylundeca-5,9-dien-2-one 7, carrying out hydroxyl halogenations, and carrying out a reaction with a pyrophosphate to obtain the geranyl acetone pyrophosphate. According to the present invention, the method has advantages of low cost, mild reaction conditions and less isomer impurities, and is suitable for scale-up production.