We used capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS) to characterize the metabolic profiles of the seed, pulp, stem and leaf of Illicium anisatum. CE-TOFMS detected more than 1000 polar metabolites within 40 min, of which 58 were annotated and quantified. Seed had higher levels of glycolytic metabolites than pulp, stem and leaf, while leaf had higher levels of TCA cycle and nucleoside metabolites. Among amino acid metabolites, levels of Gln, Glu, and Asp were higher in almost every organ. Levels of shikimic acid, the source compound for Tamiflu^®, were high in all organs, ranging from 6.84% to 28.82%. These results indicate that CETOFMS-based metabolomics offers an efficient, convenient method for comprehensive metabolite profiling, and may be a powerful tool for the screening of drug discovery.