Aim. This study investigated the association of DNA methylation with Graves' orbitopathy (GO) incidence through a combined analysis in the context of biological network to identify and validate potential genes for Chinese patients with GO. Methods. A genome-scale screening of DNA methylation was performed on the peripheral blood sample of six patients with GO and six controls. After extracting differentially methylated regions (DMRs), the study focused on two classes of genes with obviously different methylation levels: low methylated genes (LMGs) and high methylated genes (HMGs). Mutual information was applied to construct LMG- and HMG-regulated networks, and the top 10 LMGs and HMGs were extracted based on the topological properties. Then, 9 candidate genes were extracted to validate their association with GO in an expanded population (48 patients with GO vs. 24 normal controls) using single-cell methylation sequencing. Results. In the LMG-regulated network, some LMGs displayed a higher degree, such as HIST1H2AL, EFCAB1, and BOLL. Similarly, in the HMG-regulated network, some HMGs, such as MBP, ANGEL1, and LYAR, also showed a higher degree. For validation using an enlarged population, BOLL still displayed the lower methylation level whereas CDK5 and MBP still displayed the higher methylation level in patients with GO in the multivariable logistic regression analysis adjusted by age and gender (P<0.01). Conclusions. BOLL, CDK5, and MBP are potential genes associated with GO. This study was novel in clinically investigating the relation of these genomic loci with GO. The findings might provide new insights into understanding this disease.