Hepatocytes derived from human embryonic stem cells (hESCs) may be a useful source for the treatment of diseased or injured liver. However, a low survival rate of grafted hepatocytes and immune rejection are still major obstacles to be overcome. We previously showed that secreted proteins (secretome) from hESC-derived hepatocytes had a potential therapeutic power in the tissue repair of injured liver without cell transplantation. The purpose of the present study was to discover key protein(s) in the secretome of hESC-derived hepatocytes using proteomic analysis and to study the tissue repair mechanism which may be operated by the secretomes. Purified indocyanine green+ hepatocytes derived from hESCs displayed multiple hepatic features, including expression of hepatic genes, production of albumin, and glycogen accumulation. The nano-LC/ESI-QTOF-MS analysis identified 365 proteins in the secretome of hESC-derived hepatocytes and the protein functional network analysis was conducted using the MetaCore TM from GeneGO. In addition, 20 tissue regeneration-related transcription factors (TFs) were extrapolated through further proteomic analysis. After intraperitoneal injection, the secretome significantly promoted the liver regeneration in a mouse model of acute liver injury. Protein functional network analysis on the secretome-induced regenerating liver confirmed 20 transcription factors (TFs) which were identified in the ICGhigh cells. The upreguation of these tissue repair-related TFs were validated by qPCR and western blotting on the regenerating liver tissues. These results demonstrate that application of the secretome analysis in combination with the protein functional network mapping would provide a reliable tool to discover new tissue-regenerating proteins as well as to expand our knowledge of the mechanisms of tissue regeneration.