Abstract: Objective To observe the efficacy of different Chinese medicine prescriptions treating at different stages of menstrual cycle on ovarian function and pregnancy in infertile women with polycystic ovary syndrome. Methods Ninety patients with infertility PCOS who were diagnosed and met in our hospital from February, 2013 to February, 2015 were divided into control group (45 cases) and combined group (45 cases) according to the random number table method. Two groups of patients began oral estradiol cyproterone at 5th day of menstrual cycle, continuous taking 21 days, then stopping for 7 days, insisting on taking 3 menstrual cycle. After that, the control group started using citrate clomiphene tablets at 5th day of 4th menstrual cycle, insisting on taking 3 menstrual cycles. The combined group was supplemented by different Chinese medicine prescriptions according to menstrual cycle on the basis of the control group. The Sex hormone level, TCM syndrome score, endometrial thickness, dominant follicular rate, pregnancy rate and clinical efficacy between two groups were compared. Results After treatment, the levels of LH, T, FSH and E₂ in the control group were not statistically significant compared with those before treatment (P>0.05), the levels of LH, T and E₂ were significantly decreased in the observation group (P<0.05), and the FSH level was significantly increased (P<0.05), and the differences between the two groups were statistically significant (P<0.05). The clinical efficacy of the combined group was significantly higher than that of the control group (P<0.05), the endometrial thickness, the dominant follicular rate and the pregnancy rate were significantly higher than those in the control group (P<0.05). Conclusion The use of different traditional Chinese medicine prescriptions in the different stages of the menstrual cycle for the treatment of PCOS infertility has certain advantages, can improve the patients' ovarian function, improve pregnancy rate. It is worthy of clinical application.