Polycystic ovary syndrome (PCOS) is now a common gynecological endocrine disease, also known as Stein–Leventhal syndrome. Studies have found that Vaspin gene polymorphism is significantly associated with diabetes and cardiovascular disease, and PCOS has a clear glucose metabolism abnormality. So far, because the cause of PCOS is not clear, many problems such as the etiology, diagnostic criteria, prevention, and treatment of PCOS remain unsolved. Which also makes PCOS attract the attention of academic circles. Therefore, it is urgent to clarify the pathogenesis of PCOS, in order to explore the clinical correlation between the polymorphism of the Vaspin gene and polycystic ovary syndrome. This article introduces the correlation analysis study of Vaspin gene polymorphisms and polycystic ovary syndrome based on intelligent medicine. This article first selected 40 patients with PCOS as the experimental group and then selected 40 patients without PCOS as the control group. Secondly, through the detection methods of hs-CRP level detection and oil red O fat staining and passed two sets of control experiments. Finally, intelligent medical data analysis was used to analyze the location of the Vaspin gene in the experimental group and the control group. The final result showed that the correlation reached 75%.