Objective To investigate the pathogenesis of hepatocellular carcinoma (HCC) and provide the basis for its diagnosis and clinical treatment. Methods Differentially expressed miRNA and mRNA between HCC samples and adjacent tissue samples were identified based on the cancer genome atlas (TCGA) database. The target genes with differentially expressed miRNA were predicted by miRDB and TargetScan databases, and the intersection of miRNA with differentially expressed mRNA was determined. Prediction of potential transcription factors in differentially expressed miRNA in HCC using FunRich software. Functional annotation and pathway enrichment analysis were performed using the clusterProfiler package in Bioconductor. The protein-protein interaction network was constructed using a STRING database, and the miRNA-mRNA regulatory network was mapped by Cytoscape. Twenty miRNA with the most significant differential expression was verified and correlated survival analysis was performed. Results A total of 300 differentially expressed miRNA was identified in 375 HCC samples and 50 paracancerous samples by differential miRNA analysis. Totally 1106 diffe-rentially expressed mRNA was identified in differential mRNA analysis on 374 HCC samples and 50 paracancerous samples. Twenty miRNA with the most significant differential expression was selected from the up-regulated and down-regulated miRNA for target gene prediction. Functional enrichment analysis indicated that 131 candidate genes were mainly related to the regulation of valine, leucine and isoleucine degradation, carbon metabolism and prolactin signaling pathway. Conclusion The abnormally expressed miRNA-mRNA pathway in HCC may become a new biomarker for the diagnosis and provide the basis for diagnosis and clinical treatment.