Abstract: In order to comprehensively analyze the chemical composition characteristics of Zingiber neotruncatum and Amomum coriandriodorum, their primary edible parts were subjected to extensive targeted metabolomic profiling using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) were employed to screen differential metabolites. The results revealed a total of 1119 metabolites identified in both spice plants, with amino acids and their derivatives constituting the highest proportion (197 metabolites, 17.61%). Relative content analysis of primary metabolites indicated that amino acids and derivatives were the most abundant in both species, followed by organic acids, lipids, and nucleotides and their derivatives. Dominant metabolites in these categories were L-valine, succinic acid, palmitaldehyde, crotonoside (2-hydroxyadenosine) for Z. neotruncatum, and L-valine, dimethylmalonic acid, palmitaldehyde, and 2'-deoxyinosine-5'-monophosphate for A. coriandriodorum. Among secondary metabolites, alkaloids exhibited the highest abundance, followed by phenolic acids and flavonoids. Key metabolites in these classes included choline, dihydrodemethoxy curcumin, and quercetin-3-O-robinobioside in Z. neotruncatum, versus indole-3-carboxylic acid, phthalic anhydride, and luteolin-7-O-glucuronide-5-O-rhamnoside in A. coriandriodorum. Comparative analysis revealed 594 differential metabolites between the two species, with 364 up-regulated and 230 down-regulated metabolites in A. coriandriodorum relative to Z. neotruncatum. Notably, A. coriandriodorum contained 25 unique metabolites (e.g., N-acetylproline), while Z. neotruncatum possessed 15 exclusive compounds (e.g., N-(1-deoxy-1-fructosyl) tryptophan). Significant disparities were also observed in curcuminoids (e.g., curcumin, dihydrocurcumin) and 5-O-caffeoylshikimic acid. This study employed extensive targeted metabolomics to comprehensively elucidate the chemical composition and metabolic differences between Z. neotruncatum and A. coriandriodorum, identifying key components and bioactive substances. These findings provide a valuable reference for further exploration of their medicinal potential and support future research and development efforts.