The present invention discloses a cryptochlorogenic acid preparation method comprising the following steps: taking chlorogenic acid, dissolving the chlorogenic acid in methanol, then adding 1-2mol / L hydrochloric acid for the reaction while stirring for 6-8h, using a 1-2mol / L NaOH solution for adjusting pH to be neutral, concentrating, dissolved in methanol, filtering, concentrating under reduced pressure, adding water for dissolving, and filtering to obtain a filtrate; taking the filtrate for pretreatment by a reverse phase C18 column, washing with water, collecting a water washing solution, concentrating, centrifuging, filtering, and preparing cryptochlorogenic acid by reverse phase industrial preparative chromatography. According to the cryptochlorogenic acid preparation method, best acid conversion conditions and alkali neutralization reaction conditions can be obtained by screening by system experiments, the high purity cryptochlorogenic acid can be prepared by the reverse phase industrial preparative chromatography, and the method is high in yield and suitable for large-scale preparation, and achieves good technical results.