Fructus Amomi (FA) is usually regarded as the dried ripe fruits of Amomum villosum Lour. (FAL) or Amomum villosum Lour. var. xanthioides T. L.Wu et Senjenis (FALX) However, FAL, which always has a much higher price because of its better quality, is confused with FALX in the market. As volatile oil is the main constituent of FA, a strategy of chromatography-mass spectrometry (GC-MS) and chemometric approches 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 chromatograph (TIC) showed that cis-nerolidol existed only in FALX. Bornyl acetate and camphor, could be considered as the most important ones in FAL and FALX respectively. Moreover, hierarchical cluster analysis (HCA) and principal component analysis (PCA) successfully distinguished the chemical constitutes of the volatile oils in FAL and FALX. Additionally, bornyl acetate, α-cadinol, linalool, β-myrcene, camphor, d-limonene, terpinolene and endo-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 first developed a scientific approach to separate FAL and FALX based on volatile oils by GC-MS combined with chemometric techniques.