Background: Amomi fructus as edible and medicinal food can be used as a flavoring in the daily cooking and herbal tea, the consumption of A. fructus is gradually aggregate in recent years. The quality of A. fructus from Yangchun city of Guangdong province in China is familiar as the best and the value is higher than other areas, the flavor and pharmacological activities is mostly affected by its quality. However, geographical origin confusion often occurs in the market, so it is obligatory to develop technology to differentiate the geographical origin of A. fructus. Objectives: The objective of this study is to assess the antioxidant activity of A. fructus and discriminate the geographical origin of A. fructus using nontarget metabolomics technology. Materials and Methods: Ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry was used for acquired data in positive ionization modes, principal component analysis, and orthogonal partial least-squares discrimination analysis. The online analysis website Metabo Analyst 4.0 (https://www.metaboanalyst.ca/) was used for the ensuing analysis. A reducing power test, chelating power of ferrous ions test, 1,1-diphenyl-2-picryl-hydrazyl-hydrate assay, and hydroxyl radicals scavenging ability assays were used to assess the differences in antioxidant activity between the samples from the two geographical locations. Results: Eleven differential metabolites were attained, among which eight were established as marker compounds with the greatest contribution to the discernment between the two production areas. The antioxidant activity happens obvious differences due to dissimilar geographical origin. Conclusion: Untargeted metabolomics combined with multivariate statistical analysis is a commanding strategy to extricate the samples from the same species and to comprehend the quality differences from the viewpoint of overall metabolic profile.