A non-targeted metabolomics method for investigation on metabolite profiling of rice seed was developed based on gas chromatography-mass spectrometry.The extraction efficiencies of three extraction methods and four extraction solvents were investigated.Results showed that vortex and methanol-water(80∶20,by volume) were highly efficient for metabolites extraction from rice.With good stability and linearity,This method was applied in investigation on metabolite profiling of rice,including Nongda,Daohuaxiang and Zhuangyuan.It was found that they have different metabolic phenotype.Compared with Nongda,Daohuaxiang contained more contents of hexadecanoic acid,oleic acid,linoleic acid,octadecanoic acid,glucose,galactose,mannitol,asparagine and citric acid,and Zhuangyuan also had more lactic acid.Nevertheless,Nongda had more succinic acid and fructose than daohuaxiang,and more threonine than Zhuangyuan.And the contents of lactic acid,succinic acid,octadecanoic acid and fructose in Daohuaxiang were lower than those in Zhuangyuan.The developed method could be used for investigation on the metabolic phenotype of rice with different types,genotypes or habitats.It was expected to provide useful information for improving rice production and quality.