There is no specific method for the preoperative diagnosis of atypical bile duct hyperplasia, which is a precursor of cholangiocarcinoma. This study aimed to create a new model for diagnosing atypical bile duct hyperplasia based on routine laboratory tests in patients with intrahepatic lithiasis.The new diagnostic model was developed with a derivation cohort that included 375 patients with intrahepatic lithiasis. Clinical and pathological data were retrospectively collected. Prognostic factors were evaluated with univariate and logistic regression analyses. The validation cohort included 136 patients who were retrospectively screened to quantify the model's predictive value.Age and Carbohydrate Antigen 19-9 (CA-199) were revealed to be diagnostic indicators of atypical bile duct hyperplasia in patients with intrahepatic lithiasis. The new diagnostic model was created with the formula: -6.612 + (0.002 × CA-199) + (0.072 × Age). The area under the receiver operating curve of the model was 0.721. With 0.25 as the cutoff point, the sensitivity and specificity of this model in the derivation cohort were 13.9% and 95.9%, respectively. In the validation cohort, these values were 28.5% and 88.7%, respectively. The novel model has an acceptable and stable ability to predict atypical hyperplasia in the intrahepatic bile duct.This novel model provides a simple system for diagnosing atypical bile duct hyperplasia before surgery in patients with intrahepatic lithiasis.