The diagnosis of malignant biliary strictures remains a challenging aspect of biliary endoscopy. Molecular biological testing techniques based on bile have been reported to improve detection rates. However, whether the combination of bile-based omics studies and biliary brush cytology/biopsy can enhance diagnostic sensitivity has not yet been reported. This study aims to collect bile from patients with malignant biliary strictures, screen for molecular markers associated with biliary malignancies through multi-omics analysis, and subsequently validate these markers to establish a bile-based molecular diagnostic model.