Objective To investigate the relationship between polycystic ovary syndrome (PCOS) and Follicle-stimulating hormone receptor. Methods Improved qPCR based SNP detection method was developed and used in genotyping of FSHR in PCOS. Validation was performed by Sanger sequencing. Results Results showed that it could be well genotyped by this qPCR based method, and all the results were consistent with Sanger sequencing. The distribution of the allele frequency and genotype frequency were significant differences between FSHR and PCOS, which indicated that the site of Thr307Ala and Asn680Ser might be closely related with PCOS. Conclusions It proves a novel method for SNP genotyping and the results denoted important foundation for SNP detection and PCOS investigation.