Background: Intrahepatic cholangiocarcinoma (ICC), one type of highly malignant tumor, has a poor prognosis. However, the specific role of the polycystic kidney and hepatic disease 1 (PKHD1) gene in ICC has not yet been evaluated. This study aimed to investigate the potential function and mechanism of the PKHD1 gene in ICC. Methods: Quantitative real-time PCR was applied to detect the expression of PKHD1 mRNA in human ICC and adjacent normal tissues. CRISPR/Cas9 technique was used to construct PKHD1 partially knockout (PKHD1-/+) ICC cell lines. In the vitro study, the effects of PKHD1 on the malignant biological behavior of ICC cells were examined by Edu, RTCA, migration, and invasion assays. The expression levels of proteins were detected using western blotting, immunohistochemistry, and flow cytometry. Furthermore, DAPT, an antagonist of the Notch1 signaling pathway, was used in the rescue experiment in vitro. Results: Compared with normal tissues, PKHD1 mRNA expression was significantly down-regulated in human cholangiocarcinoma tissues (P<0.001). At the same time, the expressions of Notch pathway-related proteins were dramatically increased in PKHD1(-/+) ICC cells (P<0.001). Moreover, tumor proliferation, migration, and invasion were promoted in loss-of-function experiments in vitro and in vivo, which was partially reversed by DAPT. Conclusions: PKHD1 inhibits the proliferation, migration, and invasion of ICC, and the Notch pathway may be the downstream mechanism of the negative regulatory effect of PKHD1 during the progression of ICC.