Background Polycystic ovary syndrome (PCOS) is the major reason for women's low fertility and the most frequent endocrine disorder in women of childbearing age. Homocysteine is an amino acid that contains sulfur that has been negatively correlated with the reproductive outcome of polycystic women treated with IVF/ICSI. However, the impact of blood homocysteine levels on the outcome of artificial insemination in polycystic ovary syndrome women is unknown. The goal of this study is to examine the impact of serum homocysteine on the result of intrauterine insemination in females who have polycystic ovary syndrome (PCOS). Methods 96 infertile women (129 cycles) treated with artificial insemination were collected, including 66 cases (87 cycles) in the case group (PCOS group) and 30 cases (42 cycles) in the control group (male factor infertility). The differences in general data amongst two groups, such as BMI, Hcy, and age, were compared. The case group has been classified into two groups based on serum Hcy level: LHcy group (Hcy < 15) and HHcy group (Hcy ≥ 15). The relationship among pregnancy and serum Hcy level outcome in PCOS women was compared. Results The PCOS group had substantially increased serum homocysteine levels in comparison to the control group (P = 0.019). Among PCOS women, the clinical pregnancy rates of artificial insemination in the HHcy group and LHcy group were 14.29% and 37.88%. The difference among the two groups was substantial (P = 0.044). Artificial insemination frequency, ovulation induction, BMI, infertility years, AMH, serum testosterone, HOME IR, TSH, TPOAb, hCG, daily follicle size, intimal thickness, and other factors did not differ greatly between the two groups. Conclusion Serum homocysteine levels are increased in women having PCOS. Their levels above the threshold will lower the clinical pregnancy rate of intrauterine insemination in PCOS women.