Chemical constitutes of volatile oil in the rhizomes and radixes of Notopterygium incisum Ting ex H.T. chang (qianghuo in Chinese) from different regions were investigated using comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC x GC-TOFMS) and GC x GC-flame ionization detector (FID). A total of 769 compounds were tentatively identified and quantified in a typical sample from Sichuan province, a producing area of the Genuine Medicinal Materials. An obvious group-type separation was observed in the GC x GC-TOFMS chromatogram. Identification and quantitative results showed that qianghuo from Sichuan province has some significant differences in the chemical composition from other geographical origin of herbs, especially in monoterpenes and oxygenated sesquiterpenes. The data of all individual peaks collected by GC x GC-FID were processed using a principal component analysis (PCA) method to classify the samples from different regions, find and identify the marker compounds that lead to the differentiation. The abundances of monoterpenes and oxygenated sesquiterpenes were responsible for the differentiation, which is in good agreement with the group quantitative results of GC x GC analysis.