Background Lymph node metastasis (LNM) in colorectal cancer (CRC) is closely related to the choice of treatments. Given the deficiencies of conventional tests, we aim to discover novel DNA methylation markers to efficiently identify LNM status. Methods Genome-wide methylation sequencing was performed in a cohort (n = 30) using fresh CRC tissue to discover differentially methylated markers. These markers were subsequently validated with fluorescence quantitative PCR in a cohort (n = 221), and the optimal marker was singled out to compare with conventional diagnostic methods. Meanwhile, immunohistochemistry was used to verify the effectiveness of the antibody corresponding to this optimal marker in a cohort (n = 56). Results LBX2 achieved an AUC of 0.87, specificity of 87.3%, sensitivity of 75.7%, and accuracy of 81.9%, which outperformed conventional methods including imaging (CT, PET-CT) with an AUC of 0.52, CA199 with an AUC of 0.58, CEA with an AUC of 0.56. LBX2 was also superior to clinicopathological indicators including the depth of tumor invasion and lymphatic invasion with an AUC of 0.61and 0.63 respectively. Moreover, the AUC of LBX2 antibody was 0.84 in immunohistochemical validation, which was also better than these conventional methods. Conclusion In conclusion, a novel DNA methylation marker LBX2 could be used as a simple, cost-effective, easy-to-implement, and reliable diagnostic method for LNM of CRC compared to traditional methods, it holds the potential to provide a better clinical diagnosis for the precise treatment of CRC.