Artemisia annua L. is an annual herb native of Asia and this plant has been famous for the discovery of the anti-malarial drug artemisinin since 1971. In this work, to investigate variety of whole metabolites, metabolic fingerprinting analysis of A. annua L. was carried out by GC and GC-MS coupled with trimethylsilyl derivatisation. Principal component analysis and partial least squares discriminant analysis were employed to classify GC data of A. annua L. samples at five developmental stages. The results indicated that there was no distinct difference of metabolites between control (001) and transgenic strain (F4) from the tender seedling stage to adult seedling stage, but clear differences were detected at pre-flower budding stage, flower budding stage and full flowering stage. Three precursors of artemisinin biosynthesis were studied at five developmental stages and found that a possible bottleneck exists in the conversion from artemisinic acid or dihydroartemisinic acid to artemisinin.