Objective To explore the difference in the expression levels of obestatin and copeptin between patients with polycystic ovary syndrome (PCOS) and healthy women, and analyze their relationships with the risk factors of cardiovascular diseases in PCOS patients. Methods The study subjects were divided into three groups: the obese group, non-obese group and control group. The biochemical indexes and fasting insulin level were tested with biochemical analyzer and hormone automatic analyzer respectively. And the level of C-reactive protein (CRP) was measured by chemiluminescence method. ELISA was applied to test the expression levels of obestatin, copeptin and testosterone. Ultrasonic testing was used to detect carotid intima-media thickness (CIMT), and hirsutism was diagnosed according to the Ferriman-Gallwey (F-G) scoring. Blood pressure, waist-to-hip ratio (WHR) and body mass index (BMI) were all measured. Then, SPSS 11.5 software was used to analyze the relationships between obestatin, copeptin and other parameters. Results Blood pressure and CRP were higher in the non-obese group than in the control group, and higher in the obese group than in the non-obese group (P < 0.05). The F-G score and testosterone in the non-obese group were higher than those in the control group, and they  were higher in the obese group than in the non-obese group, the differences were all statistically significant (P < 0.05). The obestatin in the control group was higher in people with PCOS, and it was much lower in the obese group than in the non-obese group (P < 0.05). On the contrary, the level of copeptin was higher in the obese group than in the non-obese group (P < 0.05). Obestatin was negatively correlated with the cardiovascular risk factors; whereas copeptin was positively correlated with the cardiovascular risk factors. Conclusions  Obestatin expression level is low while copeptin expression level is high in PCOS patients, especially in obese PCOS patients. Obestatin is negatively related with the cardiovascular risk factors, and copeptin is positively related with the cardiovascular risk factors. They both have the potential to be the biomarkers of early cardiovascular diseases in PCOS patients.