Amomum villosum Lour. is a common functional food that promote intestinal health. Yangchun City is considered the best habitat for A. villosum among all producing areas in China. However, no studies have shown a difference between Yangchun and other producing areas in terms of the metabolic profiles of A. villosum fruits. The current study analyzed the metabolic profiles of A. villosum fruit samples cultivated in five representative producing areas, and explored the associations with environmental factors. A total of 969 metabolites were identified using liquid chromatography-tandem mass spectrometry (LC-MS/MS), and the potential biomarker clusters re-composed with 5 metabolites (indole-5-carboxylic acid, glutaric acid, afzelechin, 3-hydroxyanthranilic acid, and adenosine 5-diphosphate) (AUCs = 0.813-1.0) were shown to distinguish samples from different areas. OPLS-DA was performed to identify region-specific metabolites in each producing area. For the geo-authentic area (Yangchun), the prominent metabolites were mainly related to anti-inflammatory effects. Moreover, 11 environmental factors were significantly associated with the metabolites in A. villosum fruits (p < 0.05), and latitude was the highest correlation factor (r(2) = 0.351, p = 0.004). This work provides a practical strategy for detecting adulterations of the geo-authentic habitat of A. villosum, and offers a scientific basis for the assessment of habitat suitability and introduction of high-quality A. villosum.