Cistanche is the traditional and precious Chinese herbal, with two thousand years of use history in China. It has the effect on tonifying kidney, strong supplement to the liver and kidney, and replenishing essence and blood, known as the "desert ginseng". Here, we explored the mechanism of Phenylethanoid Glycosides of Cistanche (PGC) to the model mice of menopausal syndrome, as well as the therapeutic effect and characteristics of PGC to the menopausal syndrome. In this study, KM mice were reproduced by the complete resection of the ovaries on both sides of the back to establish the model mice of menopausal syndrome (MPS), and received distilled water or drugs, respectively. Model mice received distilled water. Mice received 200 mg/(kg day) high doses of Phenylethanoid Glycosides of Cistanche (HPGC), and 100 mg/(kg day) medium doses of Phenylethanoid Glycosides of Cistanche (MPGC), and 50 mg/(kg day) low doses of Phenylethanoid Glycosides of Cistanche (LPGC). After 21 days, it could determine the number of independent activities and the number of standing, the latent period of first entering the dark room, and the electric number. It also calculated the viscera index of uterus, thymus, spleen, measured the levels of estradiol (E2), testosterone (T), luteinizing hormone (LH), and follicle-stimulating hormone (FSH) in the serum. Furthermore, it observed the pathological changes of uterus, thymus, spleen and pituitary of mice. The results showed that behavioral indicators: Compared with the model group (MG), HPGC, MPGC, LPGC could increase the independent activities ( < 0.01); HPGC, MPGC could increase the number of standing, the latent period of first entering the dark room, and reduce the electric number ( < 0.01); LPGC could increase the number of standing ( < 0.05); Viscera index: Compared with MG, HPGC, MPGC could increase the viscera index of uterus, thymus, spleen ( < 0.01); LPGC could increase the viscera index of uterus ( < 0.05); Serum index: Compared with MG, all groups could decrease the levels of LH in the serum ( < 0.01); HPGC, MPGC could improve the levels of E, T and decrease the levels of LH, FSH in the serum ( < 0.01); LPGC could improve the levels of E and decrease the levels of FSH in the serum ( < 0.05). Meanwhile, it had the trend to improve the levels of T in the serum. Pathological changes: Compared with MG, HPGC could significant improve the pathological changes of uterus, thymus, spleen and pituitary of mice; other groups also has a certain effect. The results indicated that PGC could improve the sex hormone disorder of MPS, and restore the function of uterus, thymus and spleen, with better therapeutic effect on MPS.