To compare the distinction of endogenous small molecular metabolites in urine samples from the patients suffering from osteoarthritis(OA) and the healthy people. To contrast the variance of metabolic phenotypes belong to the two different TCM syndromes of OA. Methods: Urine samples of 85 participants (43 non-OA controls and 42 individuals with the disturbance of OA which include two different classes in TCM theory) were selected. Utilizing the combined gas chromatography and mass spectrometry (GC-MS) method for the detection of such urine samples. Pattern recognition was applied to analyze the raw data. Some potential biomarkers of OA were identified by means of retrieval of mass spectral database. By the same means, comparative study was carried out between the two groups of TCM syndromes. Results: Obvious differences were found in the total ion chromatograms (TIC) of urine samples between the OA and control subjects. When compared the insufficiency of liver and kidney with tendon and vessel stagnation syndrome group with the control, the plot of PCA scores showed that satisfactory separation was made. Better division was realized when the more sophisticated model PLSDA and OPLSDA were utilized. Well-pleasing separation was achieved when the comparison between of the asthenia of both spleen and kidney with dampness invading joints syndrome group and the control one as well as between of the two TCM syndromes. Conclusion: There are differences in the urine metabolite profiles among different types of syndrome of OA and the control group. The metabolic regulatory network in organism probably is perturbed in the progress of OA. The nature of types of syndrome of TCM maybe base on the variation of metabolites in vivo and the technique of metabonomics could facilitate the research of the nature of TCM theory.