Bsckground Polycystic ovary syndrome (PCOS) is a heterogeneous condition that increases the risk for serious health complications among women. Thus, in this study, we aimed to identify polymorphisms in the KiSS-1 and GPR54 genes and investigate the associations between KiSS-1, BMI, FSH, LH, and estradiol in Chinese women with PCOS.Methods This study recruited women with PCOS (n = 60) and controls (n = 60). We collected blood samples and measured endocrine indicators (kisspeptin, FSH, LH–FSH ratio, estradiol, prolactin, and testosterone). PCR and Snapshots were performed to screen single nucleotide polymorphisms (SNPs) of the KiSS-1 and GPR54 genes.Results Compared with the controls, endocrine and metabolic disturbances in women with PCOS were reflected in significantly higher levels of BMI, LH, LH–FSH ratio, prolactin, and testosterone. Serum kisspeptin levels were significantly higher and positively correlated with LH and T levels (p < 0.05). No identified SNPs of KiSS-1 and GPR54 showed significant differences in frequency between patients and controls. The mutant G allele was highly predisposed to polymorphism in the PCOS GPR54 gene r10407968. We observed a significant difference in estradiol (p = 0.023, p = 0.012) after comparing the values of LH, FSH, estradiol, progesterone, and testosterone among the three genotypes of rs4889 and rs5780218. The KiSS-1 rs4889 CC genotype and rs5780218 AA genotype showed significantly higher estradiol levels compared with the other two genotypes.Conclusions These results suggest that kisspeptin plays a potential role in the etiology of PCOS.