As one of the most diagnosed malignancies in men, prostate cancer has exhibited a high incidence rate in recent years. According to the NCCN guidelines, TNM staging of prostate cancer is an important basis for the best treatment modality. Here in this study, we established two model systems for PCa's T staging diagnosis and disease-free prediction for the first time, based on the combined analysis of WGCNA, univariate COX, and LASSO regression. Models for T staging and disease-free exhibited a high accuracy of 81.3% and 77.5% in the validation cohort, respectively. In addition, a significant negative correlation between gene expression and DNA methylation was observed in these models, which may provide new insight for further studies. Overall, our research can assist clinical diagnosis, predict the disease-free survival of patients, guide the choice of treatment options, and provide new ideas for the studies of prostate cancer.