Objective To explore the role and possible molecular mechanism of Isocitrate dehydrogenase 1(IDH1) gene in proliferation and migration of intrahepatic cholangiocarcinoma (iCCA) cell HuCCT1. Methods HuCCT1 cells with IDH1 gene knockout (HuCCT1^IDH1-/-) were constructed by CRISPR/Cas9 gene editing technology. To investigate the capacities of proliferation, migration and invasion of HuCCT1^WT (HuCCT1 cells with wild-type IDH1 gene) and HuCCT1^IDH1-/- cells, assays of CCK-8, clone formation, scratch and transwell were performed. Western blotting was used to detect the expression levels of epithelial-mesenchymal transition(EMT) associated proteins E-cadherin, N-cadherin, Vimentin, MMP-9, Wnt3a and β-catenin in two groups of cells. The transcriptome sequencing data of HuCCT1^WT and HuCCT1^IDH1-/-cells were analyzed by bioinformatics methods, Western blotting was used to verify the expression of signaling pathway-related proteins. Results Compared with HuCCT1^WT cells, HuCCT1^IDH1-/- cells showed the number of proliferation and clone formation significantly reduced (P<0.05), the proportion of cells blocked in G₂/M phase was significantly increased (P<0.01), the rate of scratch healing was significantly decreased (P<0.01), and the number of migrated cells (P<0.001) and invaded cells (P<0.05) was significantly reduced. qRT- PCR assay showed that the expression levels of IDH1, Vimentin, MMP-9 and genes related to the regulation of G₂/M cycle proliferation, Cyclin A2, Cyclin B1 and CDK1 mRNA were down-regulated in HuCCT1^IDH1-/- cells (P<0.05), and the expression of CDH1 mRNA encoding E-cadherin was up-regulated (P<0.01); Western blotting assay showed that the expression level of E-cadherin in HuCCT1^IDH1-/- cells was significantly increased (P<0.05), and the expression level of N-cadherin, Vimentin and MMP-9 protein was significantly decreased (P<0.05) than that in HuCCT1^WT cells. Data of transcriptome sequencing revealed 1476 differentially expressed genes (DEGs) between two groups of HuCCT1 cells. Go enrichment analysis showed the DEGs were significantly enriched in cell biological processes associated with inflammatory response, cell signaling and cell metabolism. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that the DEGs may be involved in some signaling pathways such as Wnt,MAPK, Rap1, Hippo and TNF, which are closely related to the regulation of proliferation and invasion of tumor cells. Western blotting verification results showed that compared with HuCCT1^WT cells, the relative expression of Wnt3a and β‑catenin proteins of HuCCT1^IDH1-/- cells was significantly decreased (P<0.05). Conclusions IDH1 gene may participate in the control of biological functions of HuCCT1 cells, including cell proliferation, migration, invasion and epithelial mesenchymal transition.The mechanism may be related to the activation of the Wnt/β-catenin signaling pathway.