This experiment studied the differentiations in the primary metabolites between Zanthoxylum echinocarpum and Z. nitidum with metabolomics technique based on GC-MS and explored the possible metabolic mechanism of phenotypic differentiation by enriching the metabolic pathways.GC-MS fingerprints of primary metabolites from Z. bechinocarpum and Z. nitidum were established.The metabolites were analyzed by similarity evaluation,principal component analysis (PCA) and orthogonal partial least squares discrimination analysis (OPLS-DA) methods.According to similarity evaluation,the primary metabolites are significantly different,which was confirmed by PCA.According to VIP > 1.0,P< 0.05 and P(corr)>0.5,5 biomarkers were selected(r>0.5),including quininic acid,D-talose,glycerol,D-glucose and D-fructose.Finally,the pathways of these differential metabolites were analyzed and constructed by MetaboAnalyst,KEGG and other tools along with metabolism database.Pathway enrichment result indicates phenylalanine pathway,fructose and mannose metabolism,glycolysis,starch and sucrose metabolism were the main different metabolic pathways,among which,phenylalanine pathway may be the main course of the number and type of alkaloids in them.So,it also can be used as an effective method to distinguish the characteristic components of Z. bechinocarpum and Z. nitidum,and laid the foundation for further study of the metabolic mechanisms.