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.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.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.These results suggest that kisspeptin plays a potential role in the etiology of PCOS.