Abstract: A metabolomic method based on gas chromatography-time-of-flight mass spectrometry(GC-TOFMS) was established for the comparative analysis of transgenic and non-transgenic rice seed to identify changes of endogenous metabolites in relation to gene modification. Insect resistant rice with foreign Bt gene and three non-transgenic rice of different genotypes were studied to display the influence of biotechnology and genetic background. Metabolic profiling data collected from GC-TOF MS was further performed with orthogonal signal correction-partial least squares analysis(OSC-PLS) to pick out the differentiations. Both genotype and gene manipulation remarkably impacted on the metabolic phenotype. Bt rice and its parent were different in some compounds including fructose, proline, tryptophan, malic acid, citric acid, tetradecanoic acid, etc.