The present invention provides one method for the preparation of pharmaceutically acceptable chlorogenic acid, which comprises the following steps: a. Treating the sample aqueous solution; b. Freezing; c. Thawing and filtering; d. Treating the residue organic phase; e. Concentrating and crystallizing; f. Choosing the number of times to repeat steps a-e according to the variability of chlorogenic acid content in samples; g. Drying. If the chlorogenic acid extract is isolated and purified using this method, water-soluble impurities and liposoluble impurities can be well removed, that allows the impurity content of final products has fulfilled the requirements for medicine; meanwhile, the procedures of this method are simple, and organic solvents can be recycled for further use, with low cost. This method can be applied for the further isolation and purification of chlorogenic acid extract obtained by various ways, especially for the preparation of pharmaceutically acceptable chlorogenic acid.