To explore the correlation between the serum homocysteine (Hcy) and anti-Mullerian hormone (AMH) levels of infertility women with polycystic ovary syndrome (PCOS) and their clinical indicators. Methods: A total of 102 infertile women with PCOS were selected in observation group and 124 healthy women who underwent physical examination were selected in control group from November 2022 to November 2023. The serum Hcy level of the women in the two groups was detected by enzyme cycle method, and the serum AMH level of the women in the two groups was detected by magnetic particle luminescence method. Pearson correlation analysis was used to investigate the correlation between the serum Hcy and AMH levels of the infertile women with PCOS and their clinical indicators. Receiver operating characteristic (ROC) curve was used to evaluate the diagnostic values of the serum Hcy and AMH levels of the infertility women for their PCOS. Results: The levels of serum Hcy (19.26±2.87μmol/L) and AMH (9.27±1.86ng/ml) of the women in the observation group were significantly higher than those (11.83±2.14μmol/L and 5.13±1.14ng/ml) of the women in the control group. The C-reactive protein (3.74 ±0.51 mg/L) level and the homeostasis model assessment of insulin resistance (HOMA-IR) value (4.15±0.82) and the luteinizing hormone (LH) level (16.44±2.75 U/L) of the women in the observation group were significantly higher than those (1.16±0.23 mg/L, 2.04±0.37 and 5.47±1.36 U/L) of the women in the control group. The levels of progesterone (0.76±0.23 ng/ml) and estradiol (71.04±8.26 pg/ml) of the women in the observation group were significantly lower than those (1.64±0.52 ng/ml and 81.32±9.58 pg/ml) of the women in the control group (all P<0.05). Pearson correlation analysis showed that the serum Hcy and AMH levels of the women with PCOS were positively correlated with their CRP level, HOMA-IR value and LH level, and were negatively correlated with their progesterone and estradiol levels (all P<0.05). The values of area under the curve (AUC) and its 95%CI of the serum Hcy and AMH levels of the infertility women for diagnosing their PCOS were 0.761 (0.750-0.812) and 0.867 (0.816-0.918). The AUC (95%CI) of the combination of the serum Hcy and AMH levels of the infertility women for diagnosing their PCOS was 0.904 (0.853-0.955). Conclusion: The abnormally elevated levels of the serum Hcy and AMH of the infertility women with PCOS are associated with their inflammatory response, glucose metabolism disorder and sex hormone levels, and the levels of the serum Hcy and AMH of the infertility women has better diagnostic efficacy for their PCOS.