The MS and multi-MS spectra of gambogic acid and gambogenic acid in positive ion detection mode were analyzed by electrospray ion trap mass spectrometry (ESI-QITMS) and their cleavage patterns were summarized. Gamboge samples were separated by a Kromasil C18 column and analyzed by HPLC-PDA and MS. Sixteen xanthones could be separated and detected, A collision induced dissociation (CID) experiment was carried out. Molecular weight and UV spectra with of these compounds were obtained. Ten xanthone compounds in Gamboge were identified by online photodiode array detection-MS(n) and by comparing with data from literature. It is expected to develop a comprehensive quality control method for this kind of compounds in commonly used herbal preparation especially in structure analysis of trace substances.