In order to research the molecular pathogenesis of hepatocellular carcinoma (HCC), firstly, gene expression profile data of HCC, which dealt with t-test method, was used and HCC’s characteristic genes were found, secondly, SAEM method was used to analyze these data combining HCC’s characteristic genes and human liver’s HNF family transcription factors ChIP-chip data, finally, transcriptional regulatory relations of HCC’s characteristic genes and HNF family transcription factors were got, furthermore the transcriptional regulatory motifs of HNF family transcription factors regulating HCC’s characteristic genes were found. All the results indicate that HNF family transcription factors regulate many HCC’s characteristic genes, a great number of those have very important functions, and multi-HNF family transcription factors regulating HCC’s characteristic genes can form feedforward loop motif and multi-input regulatory motifs.