Yin-Chen-Hao-Tang (YCHT) is recognized as a hepatoprotective agent for various types of liver diseases. Proteomics approaches were used to study hepatic and serum protein expression changes in bile duct ligated (BDL) rats following YCHT treatment for 27 days. Two-dimensional gel electrophoresis was used to analyze proteome changes. Of the proteins that exhibited changes, 17 were identified by means of matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry. The major effect of YCHT was evident in cytoskeleton related protein, plectin-1. In addition, proteins involved in metabolism of lipids were also shown to be affected, including low-density lipoprotein receptor-related protein 2 precursor (glycoprotein 330) and apolipoprotein A-I precursor (ApoA-I). Significant up-regulation of keratin 8 and 19 was found in liver tissue of BDL rats. Supplementation with YCHT also triggered alterations in the above proteins. Interestingly, YCHT treatment caused a statistically significant down-regulation in the secretion of monocyte chemoattractant protein-1 (MCP-1) and tissue inhibitor of metalloproteinase-1 (TIMP-1) in BDL rats with fibrosis. Our results suggested that YCHT may be useful for treatment of liver fibrosis because of its possible antiapoptotic properties, and the therapeutic effects of YCHT on liver diseases might be associated with its lipid biosynthesis regulation.