Data sets resulting from metabonomics or metabolic profiling experiments are becoming increasingly complex, which is hard to summarize and virsualize without appropriate tools. The use of chemometric tools, such as OSC, PCA, PLS-DA, OPLS-DA make the data dimension and interpretation much easier. Here we showed a system method based on PCA, OSC-PLS-DA for metabonomic data analysis; Furthermore, S-plot, as a visualized tool was used for the biomarkers discovery. As an example, dataset from RAC water extract administrated rats urine collected by LC/MS/MS was used to demonstrate this method. As a result, S-plot based on OSC-PLS-DA was proved to be an effective, time saving tool for data interpretation and biomarkers discovery.