Antrodia cinnamomea is a unique mushroom of Taiwan, which has been used as a traditional medicine for protection of diverse health-related conditions. Among many compounds identified in Antrodia cinnamomea, antrodia acids (antcins) belong to a unique group which bears an ergostan skeleton and so far only has been found in the A. cinnamomea. Many studies also indicated that antcins or their derivatives show some chemoprevention effects, such as anti-inflammatory and cytotoxic effects. Therefore, antcins have been regarded as signature compounds in A. cinnamomea and widely applied in research & development and quality control in A. cinnamomea related industry. Due to the lack of UV-Vis active chromophore, spectroscopic methods are not feasible to a very sensitive analysis of antcins. In this study, a novel method based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) for an efficient analysis of antcins was developed. Although LC-MS has been widely applied in biochemical analyses, the analysis of antcins is still far-from-routine mainly due to the following two reasons. (1) The most common ion source electrospray ionization (ESI) is feasible to ionize polar compounds but not suitable for hydrophobic compounds such as antcins; (2) Antcins tend to be deprotonated during the ionization process and the sensitivity for antcins detection is not applicable in a positive mode. To improve the sensitivity and convenience of antcins analysis on LC-MS, a polar, UV absorption active and easy-to-be-protonated chemical derivatization was developed for the sensitive analysis of antcins in this study. The present study showed that seven antcins can be easily modified by this reagent and the detection limit can be dramatically decreased. The quantitative analysis of antcins in some A. cinnamomea related products can be readily achieved using LC-MS/MS with a multiple reaction monitoring (MRM) mode. This method was further validated in terms of accuracy, precision, LOD and LOQ. In addition, a characteristic product ion was commonly observed from the modified antcins during the fragmentation. It was also applied in precursor ion scan for the screening of compounds containing carboxylic acid or other antcins in A. cinnamomea related products.