Colorectal cancer is one of the 3 most common cancers worldwide. In this study, a weighted network-based analysis method was proposed to explore the pathological mechanisms and prognostic targets of rectal adenocarcinoma (READ) at the deoxyribonucleic acid (DNA) methylation level. In this study, we downloaded clinical information and DNA methylation data from The Cancer Genome Atlas database. Differentially methylated gene analysis was used to identify the differential methylated genes in READ. Canonical correlation analysis was used to construct the weighted gene regulatory network for READ. Multilevel analysis and association analyses between gene modules and clinical information were used to mine key modules related to tumor metastasis evaluation. Genetic significance analysis was used to identify methylation sites in key modules. Finally, the importance of these methylation sites was confirmed using survival analysis. DNA methylation datasets from 90 cancer tissue samples and 6 paracancerous tissue samples were selected. A weighted gene regulatory network was constructed, and a multilevel algorithm was used to divide the gene co-expression network into 20 modules. From gene ontology enrichment analysis, characteristic M was related to biological processes such as the chemotaxis of fibroblast growth factors and the activation and regulation of immune cells etc and characteristic N was associated with the regulation of cytoskeleton formation, mainly microtubules and flagella, regulation of synapses, and regulation of cell mitosis. Based on the results of survival analysis, 7 key methylation sites were found closely correlated to the survival rate of READ, such as cg04441191 (microtubule-associated protein 4 [MAP4]), cg05658717 (KSR2), cg09622330 (GRIN2A), cg10698404 (YWHAG), cg17047993 (SPAG9), cg24504843 (CEP135), and cg24531267 (CEP250). Mutational and transcriptomic level studies revealed significant differences in DNA methylation, single nucleotide polymorphism, and transcript levels between YWHAG and MAP4 in normal tissues compared to tumor tissues, and differential expression of the 2 proteins in immunohistochemistry. Therefore, potential targeting drugs were screened for these 2 proteins for molecular docking, and artenimol was found to bind to MAP4 protein and 27-hydroxycholesterol to YWHAG. Our study found that key methylation sites played an important role in tumor metastasis and were associated with the prognosis of READ. Mutations and methylation may jointly regulate the transcription and translation of related genes, which in turn affect cancer progression. This may provide some new potential therapeutic targets and thoughts for the prognosis of READ.