In this study，Bt-transgenic and parental rice from two places(Wuhan and Hainan) was analyzed using gas chromatography-mass spectrometry-based metabolomics.774 chromatographic peaks were detected using GC-TOF/MS.Among them，278 metabolites，including carbohydrates，amino acids，fatty acids，organic acids and other compounds，were identified.The results showed that the difference of metabolome was not significant between the Bt-transgenic and parental rice using the principal component analysis method.Further partial least squares discriminant analysis，only two concentrations of glycerol and rhamnose were changed between Bt-transgenic and parental rice,rising 1.55 times and 3.32 times, respectively, compared to that of parental rice. The factor of producing origins of rice was investigated.15 metabolites have significant between two origins rice from Wuhan and Hainan. GC-TOF/MS-based metabolomic method was successfully used in comparative analysis of Bt-transgenic and parental rice,which suggested that it has no significant effect to transform exogenous Bt gene into rice cells，and the factor of rice producing origin is more noticeable.