Objective To analyze the differential expression of non-coding RNAs (ncRNAs) from liver tissues adjacent to hepatic cystic echinococcosis (CE) lesions and distant normal liver tissues using whole transcriptome sequencing, and perform functional annotations of differentially expressed ncRNAs, so as to explore the potential role of ncRNAs in the pathogenesis of CE. Methods Intraoperative liver tissue specimens adjacent to hepatic CE lesions and distant normal liver tissue specimen were sampled from patients with hepatic CE, and the expression profiles of microRNAs (miRNAs), circular RNAs (circRNAs), and long non-coding RNAs (lncRNAs) were detected using whole transcriptome sequencing. Differentially expressed genes were identified, and functional annotations were performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. In addition, a circRNA/lncRNA-miRNA-messenger RNA (mRNA) competing endogenous RNA (ceRNA) network was constructed using the Cytoscape software, and the expression of hub miRNAs in the network was validated using real-time quantitative reverse transcription PCR (RT-qPCR) assay. Results A total of 41 differentially expressed miRNAs were identified between the adjacent and distal tissues of hepatic CE lesions, including 8 up-regulated and 33 down-regulated miR-NAs, which were significantly enriched in biological processes of Ras signaling and neutrophil activation. Five differentially expressed circRNAs were detected, including 3 up-regulated and 2 down-regulated circRNAs, which were significantly enriched in molecular functions of hormone signaling pathways and RNA transcription regulation. A total of 447 differentially expressed lncRNAs were identified, including 200 up-regulated and 247 down-regulated lncRNAs, which were involved in cell proliferation, immune regulation, and extracellular matrix remodeling pathways. MiRNA target analysis predicted hsa-miR-27a-5p, hsa-miR-21-3p, and hsa-miR-181b-2-3p as hub nodes in the ceRNA network. RT-qPCR assay detected that the relative expression levels of ENSG00000253736, HAS2-AS1, PCSK6, hsa-miR-21-3p, hsa-miR-27a-5p, MIR23AHG, VIPR1-AS1, LINC02910, and hsa-miR-181b-2-3p were 3.00 ± 0.25, 2.75 ± 0.33, 1.01 ± 0.51, 2.65 ± 0.41, 1.01 ± 0.29, 1.10 ± 0.31, 1.05 ± 0.27, 0.25 ± 0.49, and 2.56 ± 0.35 in adjacent tissues of hepatic CE lesions, normalized to that in distant tissues from hepatic CE lesions, respectively (t = 6.21, 5.83, 7.51, 7.46, 6.12, 6.65, 7.13, 1.87 and 7.81, all P values < 0.01), which was consistent with whole transcriptome sequencing results. Conclusions Differentially expressed ncRNAs from adjacent and distal liver tissues of hepatic CE lesions may contribute to the pathological mechanisms of CE through mediating cell proliferation, immune evasion, and inflammatory responses, in which hsa-miR-27a-5p and hsa-miR-21-3p may serve as hub miRNAs.