Background: Neoadjuvant chemoradiotherapy (CRT) is standard treatment for locally advanced rectal cancer (LARC), but response varies considerably. We aimed to identify biomarkers predictive of CRT resistance. Patients and methods: Pre-treatment biopsies from 95 LARC patients were analyzed using integrated multi-omics profiling. A prediction model was developed and validated. Results: An integrative signature combining gene expression and methylation markers predicted pathological response with high accuracy (AUC 0.82). Non-responders showed activation of DNA damage repair pathways. Conclusions: Multi-omics biomarkers can identify CRT-resistant LARC patients who may benefit from alternative treatment approaches.