Ovarian cancer is one of the three most malignant tumors of the female reproductive system. At present, researchers do not know its pathogenesis, which makes the treatment effect unsatisfactory. Metabolomics is closely related to drug efficacy, safety evaluation, mechanism of action, and rational drug use. Therefore, identifying ovarian cancer-related metabolites could greatly help researchers understand the pathogenesis and develop treatment plans. However, the measurement of metabolites is inaccurate and greatly affects the environment, and biological experiment is time-consuming and costly. Therefore, researchers tend to use computational methods to identify disease-related metabolites in large scale. Since the hypothesis that similar diseases are related to similar metabolites is widely accepted, in this paper, we built both disease similarity network and metabolite similarity network and used graph convolutional network (GCN) to encode these networks. Then, support vector machine (SVM) was used to identify whether a metabolite is related to ovarian cancer. The experiment results show that the AUC and AUPR of our method are 0.92 and 0.81, respectively. Finally, we proposed an effective method to prioritize ovarian cancer-related metabolites in large scale.