Phytoalexins are induced defensive chemicals in plants in response to a number of biotic and abiotic factors such as microbes invading and UV irradiation. The function of these plant secondary metabolites is similar to that of immune system in animals. Meanwhile, they also show bioactivities such as free radical scavenging and anti- tumor effects. However, due to their low abundance and high diversity present in plants, methods for characterization and analysis of these compounds are still not well developed. In regarding of sensitivity and structural information providing, mass spectrometry is a good choice for analysis of phytoalexins. In this article, the application of MS in studying a kind of phytoalexins, polyhydroxystilbenes was discussed.