Fructus Amomi (FA) is usually regarded as the dried ripe fruit of Lour. (FAL) or Lour. var. T. L. Wu et Senjen (FALX.). However, FAL, which always has a much higher price because of its better quality, is often confused with FALX. in the market. As volatile oil is the main constituent of FA, a strategy combining gas chromatography-mass spectrometry (GC-MS) and chemometric approaches was applied to compare the chemical composition of FAL and FALX. The results showed that the oil yield of FAL was significantly higher than that of FALX. Total ion chromatography (TIC) showed that cis-nerolidol existed only in FALX. Bornyl acetate and camphor can be considered the most important volatile components in FAL and FALX., respectively. Moreover, hierarchical cluster analysis (HCA) and principal component analysis (PCA) successfully distinguished the chemical constituents of the volatile oils in FAL and FALX. Additionally, bornyl acetate, α-cadinol, linalool, β-myrcene, camphor, d-limonene, terpinolene and borneol were selected as the potential markers for discriminating FAL and FALX. by partial least squares discrimination analysis (PLS-DA). In conclusion, this present study has developed a scientific approach to separate FAL and FALX. based on volatile oils, by GC-MS combined with chemometric techniques.