Cholangiocarcinoma (CCA) is a highly malignant bile duct cancer that tends to invade and metastasize early. The epithelial–mesenchymal transition (EMT) has been implicated in cancer cell invasion and metastasis, as well as in cancer cell evasion of host immunity. In this study, we investigated the interaction between atypical protein kinase C‐iota (aPKC‐ι) and Snail in the regulation of EMT and its relationship to CCA immunosuppression. Our results demonstrated that aPKC‐ι, Snail, and infiltrated immunosuppressive cells were significantly up‐regulated in CCA tumor tissues and linked to poor prognosis. aPKC‐ι induced EMT and immunosuppression by regulating Snail in vitro and in vivo, although aPKC‐ι did not directly interact with Snail in coimmunoprecipitation experiments. To further clarify the molecular interaction between aPKC‐ι and Snail in relation to EMT, quantitative iTRAQ‐based phosphoproteomic analysis and liquid chromatography–tandem mass spectrometry were conducted to identify the substrates of aPKC‐ι‐dependent phosphorylation. Combined with coimmunoprecipitation, we showed that specificity protein 1 (Sp1) was directly phosphorylated by aPKC‐ι on Ser59 (P‐Sp1). Both Sp1 and P‐Sp1 were up‐regulated in CCA tumor tissues and associated with clinicopathological features and poor prognosis in CCA patients. Moreover, using chromatin immunoprecipitation assays, we found that P‐Sp1 regulated Snail expression by increasing Sp1 binding to the Snail promoter. P‐Sp1 also regulated aPKC‐ι/Snail‐induced EMT‐like changes and immunosuppression in CCA cells. Our findings further indicated that CCA cells with EMT‐like features appear to generate immunosuppressive natural T regulatory–like cluster of differentiation 4–positive (CD4+)CD25– cells rather than to increase CD4+CD25+ natural T regulatory cells, in part by mediating T regulatory–inducible cytokines such as transforming growth factor β1 and interleukin 2. Conclusion: These results demonstrate that aPKC‐ι promotes EMT and induces immunosuppression through the aPKC‐ι/P‐Sp1/Snail signaling pathway and may be a potential therapeutic target for CCA. (Hepatology 2017;66:1165‐1182).