Bile duct brush cytology is a widely used and essential method for evaluating biliary tract lesions, although it remains challenging for pathologists. Liquid-based preparations provide a better vision of morphology and enable the preparation of cell blocks, thereby enhancing reliability. However, the establishment of reproducible interpretation criteria and utilization of cell blocks remain limited. This study aimed to investigate the morphological features of liquid-based cytology using objective and reproducible criteria, incorporating histological findings to identify diagnostic features. In total, 151 cases were selected and 42 morphologic criteria were evaluated within representative clusters. Notably, 14 features, including conventional cytologic features, significantly differed between the benign and malignant groups. Malignant cell clusters were more likely to be irregularly shaped and have larger nuclear sizes, increased nuclear pleomorphism, a non-euchromatic chromatin pattern, and a higher nucleus-to-cytoplasm (N/C) ratio. Multinucleation and nuclear molding were observed exclusively in malignant cases. The presence of inflammatory cells did not differ significantly between benign and malignant cases. An increased N/C ratio was observed in the cell blocks and the architectural information aided in diagnosis. The application of cell blocks may be beneficial, emphasizing the significance of nuclear pleomorphism. We also categorized features by analyzing the sensitivity, specificity, and importance of various features. In summary, our study reaffirms the importance of conventional cytomorphologic features in liquid-based preparations of bile duct cytology and suggests a diagnostic approach with more objective morphologic criteria, highlighting the utility of cell blocks.