ObjectiveTo investigate the expression of exosome microRNAs (miRNAs) in bile of hepatic alveolar echinococcosis (HAE) patients with biliary tract invasion and the regulatory mechanism of differentially expressed miRNAs on target genes. MethodsBile samples were collected from 12 HAE patients who attended Qinghai University Affiliated Hospital from August 2017 to October 2018, with 6 patients in observation group (with the manifestation of biliary tract invasion) and 6 in control group (without the manifestation of biliary tract invasion). Ultracentrifugation extraction and Western blot were used to identify the structure of exosomes, the Trizol method was used to extract total RNA in exosomes, and miRNA expression profile microarray was used to identify differentially expressed miRNAs. The pathway enrichment analysis was performed to predict the target genes of biliary tract invasion based on differentially expressed miRNAs. ResultsA total of 74 differentially expressed miRNAs were identified between the observation group and the control group, among which 9 were upregulated and 65 were downregulated (｜Fold Change｜＞2). The pathway analysis showed that the target genes were mainly enriched in the pathways for tumorigenesis, phosphatidylinositol signaling system, and PTEN (FDR＜0.05). The GO annotation and enrichment analysis showed that the target genes were mainly enriched in the biological processes such as positive regulation of gene repression and regulation of cell differentiation (FDR＜0.05). ConclusionThe established expression profile of differentially expressed exosome miRNAs in bile of HAE patients with biliary tract invasion can be used as biomarkers for biliary tract invasion of HAE and preliminarily elaborate on the regulatory mechanism of differentially expressed miRNAs on target genes after HAE invades the biliary tract.