In many organs, including liver, cancer may originate from the organ stem or progenitor compartments. Liver progenitor cells (LPC) in the canals of Hering may be considered as the cellular origin of hepatocellular carcinoma (HCC) in many previous studies. However, characterization and identification of liver progenitor cells remains elusive. Here, we direct human embryonic stem (ES) cells differentiate to hepatic-like cell in vitro by addition of growth factors (Activin, FGF, BMP, HGF, OSM and Dex) to cultures with appropriate duration of exposure. The four stages cells of in vitro hepatic differentiation model, ES, definitive endoderm (DE), LPC and hepatocyte-like cells, were acquired and used for transcriptome sequencing. Transcriptome sequencing results revealed that human ES cell could efficiently generate DE cells, LPC and hepatic-like cells as stage sepecifc genes were highly expressed in the corresponding stage but downregulated in other stages. Furthermore, a group of genes specifically expressed in the stage of LPC was identified. Those genes could regulate the specific hepatic development signaling pathways and widely known markers of HCC stem cells, such as CD133, EPCAM and Lgr5. Thus, characterization of those genes specifically expressed in LPC may shed a light on understanding of origin of HCC and related cancer stem cells.