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Over the decades, there have been continuous efforts to enhance the quality of human life. Postmenopausal syndrome is a serious concern for the wellbeing of a woman's health. Hormonal therapy is currently the mainstay of treatment for this condition. However, this therapy could lead to estrogen abuse, leading to adverse reactions and side effects. As a result, hormonal therapy has been unsuccessful in ameliorating postmenopausal syndrome. Cistanche deserticola is a classical tonic herb in traditional Chinese medicine. It exhibits significant estrogenic activity. The main active compounds of this herb are glycosides. In a previous experiment, three important factors contributing to the total glycoside yield, acteoside yield, and estrogenic activity were identified, namely, eluent concentration, pH, and eluent volume. In this experiment, an optimal purification process was determined using a central composite design-response surface methodology to obtain glycosides from this herb. An eluent (ethanol) concentration of 85% and volume of 25 BV at a pH of 11 was found to be optimal. Twenty-one active compounds were identified by a high-performance liquid chromatography/ quadrupole time-of-flight mass spectrometry assay. This study provides valuable insights for further in-depth research evaluating the estrogenic activities of total glycosides of Cistanche deserticola.