Metabonomics methods have been successfully applied to the drug discovery, toxicology, phytochemistry, and clinical fields. Here, we report a self-developed metabonomics platform which is based on high performance liquid chromatography-mass spectrometry (HPLC-MS) technique and applied to the investigation of acute deterioration of liver function in chronic hepatitis B to find the potential biomarkers. Sera from 50 healthy persons and 37 patients with acute deterioration of liver function in chronic hepatitis B were analyzed by HPLC-MS after removal of proteins. After de-noise, peak detection and peak alignment, the data of metabolites were fed to partial least squares discriminant analysis (PLS-DA) to find the potential biomarkers. According to the corresponding tandem mass results, several potential biomarkers were identified: Lysophosphatidyl Choline (LPC) C18:0, LPC C16:0, LPC C18:1, LPC C18:2, and glycochenodeoxycholic acid (GCDCA) (or its isomer glycodeoxycholic acid (GDCA)). On the basis of the relevant literature and pathway databases, the biological significance of the present study is discussed.